Kallikrein-binding “Kunitz domain” proteins and analogues thereof

ABSTRACT

This invention provides: novel protein homologous of a Kunitz domain, which are capable of binding kallikrein; polynucleotides that encode such novel proteins; and vectors and transformed host cells containing these polynucleotides.

Related Applications

This application is a continuation application of U.S. application Ser.No. 11/365,438, filed Mar. 1, 2006, now U.S. Pat. No. 7,628,983; whichis a continuation application of U.S. application Ser. No. 10/016,329,filed Oct. 26, 2001, now abandoned; which is a divisional application ofU.S. application Ser. No. 09/421,097, filed Oct. 19, 1999, now U.S. Pat.No. 6,333,402; which is a divisional application of U.S. applicationSer. No. 08/208,264, filed Mar. 10, 1994, now U.S. Pat. No. 6,057,287;which is a continuation-in-part application of U.S. application Ser. No.08/179,964, filed Jan. 11, 1994, now abandoned, the entirety of whichare hereby incorporated by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to novel classes of proteins and proteinanalogues which bind to and may inhibit kallikrein.

2. Description of the Background Art

Kallikreins are serine proteases found in both tissues and plasma.Plasma kallikrein is involved in contact-activated (intrinsic pathway)coagulation, fibrinolysis, hypotension, and inflammation. (See Bhoola,et al. (BHOO92)). These effects of kallikrein are mediated through theactivities of three distinct physiological substrates:

i) Factor XII (coagulation),

ii) Pro-urokinase/plasminogen (fibrinolysis), and

iii) Kininogens (hypotension and inflammation).

Kallikrein cleavage of kininogens results in the production of kinins,small highly potent bioactive peptides. The kinins act through cellsurface receptors, designated BK-1 and BK-2, present on a variety ofcell types including endothelia, epithelia, smooth muscle, neural,glandular and hematopoietic. Intracellular heterotrimeric G-proteinslink the kinin receptors to second messenger pathways including nitricoxide, adenyl cyclase, phospholipase A₂ and phospholipase C. Among thesignificant physiological activities of kinins are: (i) increasedvascular permeability; (ii) vasodilation; (iii) bronchospasm; and (iv)pain induction. Thus, kinins mediate the life-threatening vascular shockand edema associated with bacteremia (sepsis) or trauma, the edema andairway hyperreactivity of asthma, and both inflammatory and neurogenicpain associated with tissue injury. The consequences of inappropriateplasma kallikrein activity and resultant kinin production aredramatically illustrated in patients with hereditary angioedema (HA). HAis due to a genetic deficiency of C1-inhibitor, the principal endogenousinhibitor of plasma kallikrein. Symptoms of HA include edema of theskin, subcutaneous tissues and gastrointestinal tract, and abdominalpain and vomiting. Nearly one-third of HA patients die by suffocationdue to edema of the larynx and upper respiratory tract. Kallikrein issecreted as a zymogen (prekallikrein) that circulates as an inactivemolecule until activated by a proteolytic event. Genebank entry P03952shows Human Plasma Prekallikrein.

Mature plasma Kallikrein contains 619 amino acids. Hydrolysis of asingle Arg-Ile bond (at positions 371-372) results in the formation of atwo-chain proteinase molecule held together by a disulfide bond. Theheavy chain (371 amino acids) comprises four domains arranged insequential tandems of 90-91 residues. Each of the four domains isbridged by 6 half-cysteine residues, except the last one, which carriestwo additional half-cysteine residues to link together the heavy andlight chains. These domains are similar in sequence to factor XI. Thelight chain (248 residues) carries the catalytic site, and the catalytictriad of His-415, Asp-464 and Ser-559 is especially noteworthy.

The most important inhibitor of plasma kallikrein (pKA) in vivo is theC1 inhibitor; see SCHM87, pp. 27-28. C1 is a serpin and forms anirreversible or nearly irreversible complex with pKA. Although bovinepancreatic trypsin inhibitor (BPTI) (SEQ ID NO: 1) was first said to bea strong pKA inhibitor with K_(i)=320 pM (AUER88), a more recent report(Berndt, et al., Biochemistry, 32:4564-70, 1993) indicates that its Kifor plasma Kallikrein is 30 nM (i.e., 30,000 pM). The G36S mutant had aKi of over 500 nM.

“Protein engineering” is the art of manipulating the sequence of aprotein in order to alter its binding characteristics. The factorsaffecting protein binding are known, but designing new complementarysurfaces has proved difficult. Although some rules have been developedfor substituting side groups, the side groups of proteins are floppy andit is difficult to predict what conformation a new side group will take.Further, the forces that bind proteins to other molecules are allrelatively weak and it is difficult to predict the effects of theseforces.

Nonetheless, there have been some isolated successes. Wilkinson et al.reported that a mutant of the tyrosyl tRNA synthetase of Bacillusstearothermophilus with the mutation Thr₅₁-Pro exhibits a 100-foldincrease in affinity for ATP. Tan and Kaiser and Tschesche et al. showedthat changing a single amino acid in a protein greatly reduces itsbinding to trypsin, but that some of the mutants retained the parentalcharacteristic of binding to an inhibiting chymotrypsin, while othersexhibited new binding to elastase.

Early techniques of mutating proteins involved manipulations at theamino acid sequence level. In the semisynthetic method, the protein wascleaved into two fragments, a residue removed from the new end of onefragment, the substitute residue added on in its place, and the modifiedfragment joined with the other, original fragment. Alternatively, themutant protein could be synthesized in its entirety.

With the development of recombinant DNA techniques, it became possibleto obtain a mutant protein by mutating the gene encoding the nativeprotein and then expressing the mutated gene. Several mutagenesisstrategies are known. One, “protein surgery”, involves the introductionof one or more predetermined mutations within the gene of choice. Asingle polypeptide of completely predetermined sequence is expressed,and its binding characteristics are evaluated.

At the other extreme is random mutagenesis by means of relativelynonspecific mutagens such as radiation and various chemical agents, seeLehtovaara, E. P. Appln. 285,123, or by expression of highly degenerateDNA. It is also possible to follow an intermediate strategy in whichsome residues are kept constant, others are randomly mutated, and stillothers are mutated in a predetermined manner. This is called“variegation”. See Ladner, et al. U.S. Pat. No. 5,220,409.

The use of site-specific mutagenesis, whether nonrandom or random, toobtain mutant binding proteins of improved activity, is known in theart, but does not guarantee that the mutant proteins will have thedesired target specificity or affinity. Given the poor anti-kallikreinactivity of BPTI, mutation of BPTI or other Kunitz domain proteins wouldnot have been considered, prior to the present invention, a preferredmethod of obtaining a strong binder, let alone inhibitor, of kallikrein.

SUMMARY OF THE INVENTION

The present invention relates to novel Kunitz domain proteins,especially LACI homologues, which bind to, and preferably inhibit, oneor more plasma (and/or tissue) kallikreins, and to the therapeutic anddiagnostic use of these novel proteins.

A specific, high affinity inhibitor of plasma kallikrein (and, whereneeded, tissue kallikrein) will demonstrate significant therapeuticutility in all pathological conditions mediated by kallikrein, andespecially those associated with kinins. The therapeutic approach ofinhibiting the catalytic production of kinins is considered preferableto antagonism of kinin receptors, since in the absence of kallikreininhibition, receptor antagonists must compete with continuous kiningeneration. Significantly, genetic deficiency of plasma kallikrein isbenign and thus, inhibition of plasma kallikrein is likely to be safe.We have recently discovered a lead pKA inhibitor, designated KKII/3#6(SEQ ID NO:7). This inhibitor is a variant of a naturally occurringhuman plasma protein Kunitz domain and demonstrates significantlygreater kallikrein binding potency than Trasylol. KKII/3#6 (SEQ ID NO:7)has a Ki for kallikrein which is over 100 times that of both wild-typeLACI (SEQ ID NO:25) and of BPTI (SEQ ID NO:1), and is in the nanomolarrange. In contrast, its Ki for plasmin is 10 uM. A reversible inhibitoris believed to be of greater utility than an irreversible inhibitor suchas the C1 inhibitor.

The present invention also relates to protein and non-protein analogues,designed to provide a surface mimicking the kallikrein-binding site ofthe proteins of the present invention, which likewise bind kallikrein.These are termed “conformational analogues.”

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows six pseudopeptide bonds, in each figure, R₁ and R₂ are theside groups of the two amino acids that form the pseudodipeptide. If,for example, the dipeptide to be mimicked is ARG-PHE, thenR₁=—(CH₂)₃—NH—C—(NH₂)₂+ and R₂=—CH₂—C₆H₅. The pseudopeptides are notlimited to side groups found in the twenty genetically encoded aminoacids.

-   -   a) ψ1(X₁,X₂,R₁,R₂) shows two α carbons joined by a trans        ethylene moiety,        -   X₁ and X₂ may independently be any group consistent with the            stability of the vinyl group; for example, X₁ and X₂ may be            picked from the set comprising            -   {H, -alkyl (methyl, ethyl, etc.), —O-alkyl (especially                methyl), —O-fluoroalkyl (—O—CF₃, —O—CF₂—CF₃), halo (F,                Cl, and Br), -fluoroalkyl (e.g. —CF₃, —CF₂—CH₃, —C₂F₅),                and secondary amine (such as N,N dimethyl)};        -   preferred X₁ groups are electronegative such as —O-alkyl and            F or hydrogen; preferred X₂ groups are H, alkyl, and            secondary amines,    -   b) “ψ2(X₁,X₂,X₃,X₄,R₁,R₂)” shows two α carbons joined by a        ketomethylene moiety,        -   X₁ and X₂ may independently be any group consistent with the            stability of the ketomethylene group; for example, X₁ and X₂            may be picked from the set comprising one of            -   {H, alkyl, amino, alkyl amino, —OH, —O-alkyl, —NH—COH,                and F};        -   preferred X₁ and X₂ groups are H, methyl, —NH₂, —OH, and F            (α fluoroketones are not nearly so reactive as are chloro            and bromo ketones);        -   X₃ and X₄ may independently by any one of            -   {H and alkyl (especially methyl)};        -   H is preferred, but alkyl groups may be used to limit the            flexibility of the peptide chain,    -   c) “ψ3(X₁,X₂,X₃,X₄,X₅,X₆,R₁,R₂)” shows two a carbons joined by        two methylene groups,        -   X₁, X₂, X₃, and X₄ may independently be any group consistent            with the stability of the bismethylene group; for example,            X₁, X₂, X₃, and X₄ may be picked from the set comprising            -   {H, —O-alkyl (especially methyl), F, Cl, Br, -alkyl                (methyl, ethyl, etc.), hydroxy, amino, alkyl hydroxy                (—CH₂—OH, —CH(CH₃)OH), alkyl amino, and secondary amino                (such as N,N dimethyl)};        -   X₅ and X₆ may be independently picked from the set            comprising            -   {H, alkyl, arylalkyl (e.g. —CH₁—C₆H₅), alkyl hydroxy,                alkyl amino, aryl, alkylaryl (e.g. p-C₆H₄—CH₂—CH₃)}.    -   d) “ψ4(X₁,X₂,X₃,X₄,R₁,R₂)” shows two a carbons joined by        —CO—C(X₁)(X₂)—NH—,        -   X₁ and X₂, may independently be any group consistent with            the stability of the aminomethylketo group; for example, X₁            and X₂ may be picked from the set comprising            -   {H, alkyl, amino, alkyl amino, —OH (but not two                hydroxyls), —O-alkyl, and F},        -   alternatively, X₁ and X₂ can be combined as the oxygen atom            of an α keto carboxylic acid group (that is, the first            residue is a β amino keto acid);        -   X₃ and X₄ may be independently picked from the set            comprising            -   {H, alkyl, alkyl hydroxy, alkyl amino, aryl, alkylaryl                (e.g. —CH₂—C₆H₅)}, hydrogen is preferred, but larger                groups may be used to limit the flexibility and                reactivity of the peptide main chain.    -   e) “ψ5(X₁,X₂,X₃,X₄,X₅,R₁,R₂)” shows two a carbons joined by a        methylene-amine group;        -   X₁ and X₂ may be any group consistent with stability of the            amine group; preferably, X₁ and X₂ may be picked            independently from the set            -   {H, alkyl (methyl, ethyl, n-propyl, isopropyl, up to                about C₆), —OH (but X₁ and X₂ can not both                simultaneously be —OH), —O-alkyl (methyl, ethyl,                n-propyl, isopropyl, up to about C₆)},        -   X₃ can be any group consistent with being a stable            substituent on a tertiary or secondary amine, preferably X₃            is picked from the set            -   {H, alkyl (C₁ up to about C₆), alkylhydroxy (—CH₂—OH,                —CH₂—CH₂—OH, up to about —C₆O₂H₁₃)};        -   X₄ and X₅ may be independently picked from the set            comprising            -   {H, alkyl, alkyl hydroxy, alkyl amino, aryl, alkylaryl                (e.g. —CH₂—C₆H₅)}, hydrogen is preferred, but other                groups may be used to limit the flexibility and                reactivity of the peptide main chain.    -   f) “ψ6(X₁,X₂,X₃,X₄,R₁,R₂)” shows two a carbons joined by a        vinylketone group;        -   X₁ and X₂ may be any group consistent with stability of the            compound; preferably, X₁ and X₂ may be picked independently            from the set            -   {H, alkyl (methyl, ethyl, n-propyl, isopropyl, up to                about C), —O-alkyl (methyl, ethyl, n-propyl, isopropyl,                up to about C₆), alkylhydroxy (—CH₂—OH, —CH₂—CH₂—OH, up                to about —C₆O₂H₁₃)},        -   X₃ and X₄ may be independently picked from the set            comprising            -   {H, alkyl, alkyl hydroxy, alkyl amino, aryl, alkylaryl                (e.g. —CH₂—C₆H₅)}, hydrogen is preferred, but other                groups may be used to limit the flexibility and                reactivity of the peptide main chain.

FIG. 2 shows six additional pseudopeptide linkages:

-   -   a) “ψ7(X₁,X₂,R₁,R₂)”, a bisketone;        -   X₁ and X₂ may be independently picked from the set            comprising            -   {H, alkyl, alkyl hydroxy, alkyl amino, aryl, alkylaryl                (e.g. —CH₂—C₆H₅)}, hydrogen is preferred, but other                groups may be used to limit the flexibility and                reactivity of the peptide main chain.    -   b) “ψ8(X₁,X₂,X₃,X₄,X₅,R₁,R₂)”, a cyclohexenone derivative:        -   X₁ can be any of            -   {H, —O-alkyl (especially methyl), F, -alkyl (methyl,                ethyl, etc.), and secondary amine (such as N,N                dimethyl)};        -   X₂, X₃, X₄, and X₅ may be picked independently from the set            -   {H, —OH (but not two hydroxyls on the same carbon),                alkyl (methyl, ethyl, n-propyl, isopropyl, up to about                C₆), —O-alkyl, —O-alkylaryl (e.g. —O—CH₂—C₆H₅),                alkylhydroxy (—CH₂—OH, —CH₂—CH₂—OH, etc.), F, Cl, Br, I,                aryl, arylalkyl, —S-alkyl} (X₄ and X₅ should not be Cl,                Br, or I).    -   c) “ψ9(X₁,X₂,X₃,X₄,X₅,X₆,R₁,R₂)”, a cyclohexone derivative:        -   X₁, X₂, X₃, X₄, X₅, and X₆ can independently be any of            -   {H, hydroxy (but not two hydroxyl groups on one carbon),                —O-alkyl (especially methyl), F, -alkyl (methyl, ethyl,                etc.), and secondary amine (such as N,N dimethyl)}    -   d) “ψ10(X₁,X₂,X₃,X₄,X₅,R₁,R₂)”, a β amino acid derivative:        -   X₁ and X₅ may be independently picked from the set            comprising            -   {H, alkyl, alkyl hydroxy, alkyl amino, aryl, alkylaryl                (e.g. —CH₂—C₆H₅)}; H is preferred.        -   X₂ and X₃ can independently be picked from the set:            -   {H, methyl, ethyl, n-propyl, isopropyl, n-butyl,                isobutyl, s-butyl, t-butyl, other alkyls up to C₆, —OH,                —O-methyl, —CH₂—OH); alternatively, X₂ and X₃ can be a                single double-bonded group, such as ═O, ═N-alkyl, or                ═C(X₆)(X₇) (where X₆ and X₇ may be H or methyl)},        -   X₄ can be            -   {H, alkyl, aryl, or substituted hydrocarbon chains}.    -   e) “ψ11(X₁,X₂,X₃,R₁,R₂)”, an imine derivative:        -   X₁ can be any group consistent with the imine bond:            -   {H, methyl, alkyl(up to C₆), —O-methyl, —O-ethyl},        -   X₂ and X₃ may be independently picked from the set            comprising            -   {H, alkyl, alkyl hydroxy, alkyl amino, aryl, alkylaryl                (e.g. —CH₂—C₆H₅)}.    -   f) “ψ12(X₁,X₂,X₃,X₄,R₁,R₂)”, an ether derivative:        -   X₁ and X₄ may be independently picked from the set            comprising            -   {H, alkyl, alkyl hydroxy, alkyl amino, aryl, alkylaryl                (e.g. —CH₂—C₆H₃)}.        -   X₂ and X₃ may be picked independently from the set            -   {H, —OH (but not two hydroxyls on the same carbon),                alkyl (methyl, ethyl, n-propyl, isopropyl, up to about                C₆), —O-alkyl, —O-alkylaryl (e.g. —O—CH₂—C₆H₅),                alkylhydroxy (—CH₂—OH, —CH₂—CH₂—OH, etc.), F, Cl, Br, I,                aryl, arylalkyl, —S-alkyl}.

FIG. 3 shows a number of amino acids that can be used to create cyclicpeptides by joining the side groups:

(A) shows L-2-(6-aminomethylnaphthyl)alanine,

(B) shows L-2-(6-carboxymethylnaphthyl)alanine,

(C) shows the crosslink generated by joiningL-2-(6-aminomethylnaphthyl)alanine toL-2-(6-carboxymethylnaphthyl)alanine by a peptide bond between thesubstituents on the 6 positions (the 6 position of naphthylene),

(D) shows L-4-(2-(6-aminomethylnaphthyl))-2-aminobutyric acid,

(E) shows L-4-(2-(6-carboxymethylnaphthyl))-2-aminobutyric acid, and

(F) shows the crosslink generated by joining (D) to (E) through thesubstituents on the 6 position of each naphthene group.

FIG. 4 shows additional compounds that can be used to close a cyclicpeptide:

-   -   (A) shows L-2-(4-oxymethyl-6-aminomethylnaphthyl)alanine,    -   (B) shows        L-2-(6-carboxymethyl-7-hydroxy-5,6,7,8-tetrahydronaphthyl)alanine,    -   (C) shows        L-4-(2-(6-carboxy-1,2,3,4-tetrahydronaphthyl))-2-aminobutyric        acid,    -   (D) shows 2,6 biscarboxymethylnaphthylene,    -   (E) shows 2,6 bisaminomethylnaphthylene, the separation between        nitrogens is about 8.5 Å.

FIG. 5 shows intermediates leading to an ethylene pseudopeptide and aornithine=alanine pseudopeptide.

FIG. 6 shows compounds 4.1 and 4.2 according to formula 4. Cmpd 4.1 hasa linker comprising —CH₂—(O—CH₂—CH₂)₃—CH₂—; the pseudopeptide is afluoroethylene group. Cmpd 4.2 has a linker derived from transcyclohexanedimethanol and ethyleneglycol units and a ketomethylene groupas pseudopeptide.

FIG. 7 shows compounds 4.3 and 4.4 according to formula 4. Cmpd 4.3 hasa 1,1-difluoroethane group as pseudopeptide and a linker comprising a2,5 dialkyl benzoic acid linker. Cmpd 4.4 has an imino group aspseudopeptide and a peptide linker Gly-Pro-Thr-Val-Thr-Thr-Gly (SEQ IDNO:30).

FIG. 8 shows compounds 4.6 (in which the linker contains a p-phenylgroup and a carboxylic acid side group) and 4.7 (in which the linkercomprises GLY-PRO-GLY-GLU-CYS-NH₂) (SEQ ID NO:32) according to formula4.

FIGS. 9A and 9B shows a hypothetical plasma kallikrein inhibitor. PanelB shows a precursor comprisingH-HIS-CYS-LYS-ALA-ASN-HIS-glutamylaldehyde (SEQ IDNO:33):1-(4-bromo-n-butane). Panel A shows the compound formed byreciprocal coupling of the butane moiety to the thiol of a secondmolecule of the compound in panel B.

FIG. 10A-D shows molecules useful for cyclizing a peptide.

-   -   A) shows a diacylaminoepindolidione (KEMP88b), the “exterior”        nitrogens are separated by about 13 Å,    -   B) shows diaminoepindolidione joined to a peptide through the        side groups of two GLU residues,    -   C) shows carboxymethylaminoaminoepindolidione,    -   D) shows carboxymethylaminoaminoepindolidione joined to the ends        of a peptide to form a loop.

FIG. 11A-H shows amino acids that favor a reverse turn,

-   -   A) 2-carboxy-8-aminomethylnaphthylene,    -   B) 2-carboxy-8-amino-5,6,7,8-tetrahydronaphthalene,    -   C) 1-carboxy-2-aminocyclopentane,    -   D) tetrahydroisoquinolin carboxylic acid (TIC)    -   E) 2-carboxy-7-aminoindan,    -   F) 2-carboxy-8-amino-7,8-dihydroxynaphthalene,    -   G) 2,5,7-trisubstituted        2(S)-5-H-6-oxo-2,3,4,4a,7,7a-hexahydropyrano[2,3-b]pyrrole        (CURR93), and    -   H) 4-(2-aminoethyl)-6-dibenzofuranpropionic acid (DIAZ93).

FIG. 12A-D shows compounds that force a reverse turn in a peptide chain:

-   -   A) 4-(2-aminomethyl-6-dibenzofuranethanoic acid,    -   B) 8-aminomethyl-5,6,7,8-tetrahydro-2-naphthoic acid,    -   C). Compound attributed to Freidinger et al. (FREI82) in NAGA93,    -   D) Compound attributed to Nagai and Sato (NAGA85) in NAGA93.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

A large number of proteins act as serine protease inhibitors by servingas a highly specific, limited proteolysis substrate for their targetenzymes.

In many cases, the reactive site peptide bond (“scissile bond”) isencompassed in at least one disulfide loop, which insures that duringconversion of virgin to modified inhibitor the two peptide chains cannotdissociate.

A special nomenclature has evolved for describing the active site of theinhibitor. Starting at the residue on the amino side of the scissilebond, and moving away from the bond, residues are named P1, P2, P3, etc(SCHE67). Residues that follow the scissile bond are called P1′, P2′,P3′, etc. It has been found that the main chain of protein inhibitorshaving very different overall structure are highly similar in the regionbetween P3 and P3′ with especially high similarity for P2, P₁ and P1′(LASK80 and works cited therein). It is generally accepted that eachserine protease has sites S1, S2, etc. that receive the side groups ofresidues P1, P2, etc. of the substrate or inhibitor and sites S1′, S2′,etc. that receive the side groups of P1′, P2′, etc. of the substrate orinhibitor (SCHE67). It is the interactions between the S sites and the Pside groups that give the protease specificity with respect tosubstrates and the inhibitors specificity with respect to proteases.

The serine protease inhibitors have been grouped into families accordingto both sequence similarity and the topological relationship of theiractive site and disulfide loops. The families include the bovinepancreatic trypsin inhibitor (Kunitz), pancreatic secretory trypsininhibitor (Kazal), the Bowman-Birk inhibitor, and soybean trypsininhibitor (Kunitz) families. (In this application, the term “Kunitz”will be used to refer to the BPTI family and not the STI family.) Someinhibitors have several reactive sites on a single polypeptide chain,and these distinct domains may have different sequences, specificities,and even topologies. One of the more unusual characteristics of theseinhibitors is their ability to retain some form of inhibitory activityeven after replacement of the P1 residue. It has further been found thatsubstituting amino acids in the P₅ to P₅′ region, and more particularlythe P3 to P3′ region, can greatly influence the specificity of aninhibitor. LASK80 suggested that among the BPTI (Kunitz) family,inhibitors with P1 Lys and Arg tend to inhibit trypsin, those withP1=Tyr, Phe, Trp, Leu and Met tend to inhibit chymotrypsin, and thosewith P1=Ala or Ser are likely to inhibit elastase. Among the Kazalinhibitors, they continue, inhibitors with P1=Leu or Met are stronginhibitors of elastase, and in the Bowman-Kirk family elastase isinhibited with P1 Ala, but not with P1 Leu.

All naturally occurring Kunitz Domain proteins have three disulfidebonds, which are topologically related so that the bonds are a-f, b-d,and c-e (“a” through “f” denoting the order of their positions along thechain, with “a” being closest to the amino-terminal), and the bindingsite surrounding or adjoining site “b”. The term “Kunitz domain protein”is defined, for purposes of the present invention, as being a proteaseinhibitor which has this fundamental disulfide bond/binding sitetopology, with the proviso that one of the disulfide bondscharacteristic of the naturally occurring protein can be omitted.

Aprotinin-like Kunitz domains (KuDom) are structures of about 58(typically about 56-60) amino acids having three disulfides: C5-C55,C14-C38, and C30-C51. KuDoms may have insertions and deletions of one ortwo residues. All naturally occurring KuDoms have all three disulfides.Engineered domains having only two have been made and are stable, thoughless stable than those having three. All naturally occurring KuDoms haveF₃₃ and G₃₇. In addition, most KuDoms have (with residues numbered toalign with BPTI) G₁₂, (F, Y, or W) at 21, Y or F at 22, Y or F at 23, Yor W at 35, G or S at 36, G or A at 40, N or G at 43, F or Y at 45, andT or S at 47.

The archetypal KuDom, bovine pancreatic trypsin inhibitor (BPTI, a.k.a.aprotonin), is a 58 a.a. serine proteinase inhibitor. Under thetradename TRASYLOL, it is used for countering the effects of trypsinreleased during pancreatitis. Not only is its 58 amino acid sequenceknown, the 3D structure of BPTI has been determined at high resolutionby X-ray diffraction, neutron diffraction and by NMR. One of the X-raystructures is deposited in the Brookhaven Protein Data Bank as “6PTI”[sic]. The 3D structure of various BPTI homologues (EIGE90, HYNE90) arealso known. At least sixty homologues have been reported; the sequencesof 59 proteins of this family are given in Table 13 of Ladner, U.S. Pat.No. 5,233,409 and the amino acid types appearing at each position arecompiled in Table 15 thereof. The known human homologues include domainsof Lipoprotein Associated Coagulation Inhibitor (LACI) (WUNT88, GIRA89),Inter-α-Trypsin Inhibitor and the Alzheimer beta-Amyloid PrecursorProtein (APP-I). Circularized BPTI and circularly permuted BPTI havebinding properties similar to BPTI. Some proteins homologous to BPTIhave more or fewer residues at either terminus. Kunitz domains are seenboth as unitary proteins (e.g., BPTI) and as independently foldingdomains of larger proteins.

LACI is a human phosphoglycoprotein inhibitor with a molecular weight of39 kDa. It includes three Kunitz domains.

The cDNA sequence of LACI (SEQ ID NO:25) was determined by Wun et al.,J. Biol. Chem. 263 6001-6004 (1988). Mutational studies have beenundertaken by Girard et al., Nature 338 518-520 (1989), in which theputative P1 residues of each of the three kunitz domains contained inthe whole LACI molecule were altered from Lys36 to Ile, Arg107 to Leu;and Arg199 to Leu respectively. It has been proposed that kunitz domain2 is required for efficient binding and inhibition of Factor Xa, whiledomains 1 and 2 are required for inhibition of Factor VIIa/Tissue Factoractivity. The function of LACI kunitz domain 3 is as yet uncertain.

In a preferred embodiment, the KuDom of the present invention issubstantially homologous with the first Kunitz Domain (K₁) of LACIresidues 50-107 of SEQ ID NO:25), with the exception of thekallikrein-binding related modifications discussed hereafter. Forprophylaxis or treatment of humans, since BPTI is a bovine protein andLACI is a human protein, the mutants of the present invention arepreferably more similar in amino acid sequence to LACI (K1) (residues50-107 of SEQ ID NO:25) than to BPTI, to reduce the risk of causing anadverse immune response upon repeated administration.

The amino acid sequence of these mutant LACI domains has been numbered,for present purposes, to align them with the amino acid sequence ofmature BPTI, in which the first cysteine is at residue 5 and the last atresidue 55.

Most naturally occurring Kunitz domains have disulfides between 5:55,14:38, and 30:51. Drosophila funebris male accessory gland proteaseinhibitor (GeneBank accession number P11424) has no cysteine at position5, but has a cysteine at position −1 (just before typical position 1);presumably this forms a disulfide to CYS⁵⁵. Engineered Kunitz domainshave been made in which one or another of the disulfides have beenchanged to a pair of other residues (mostly ALA). Proteins having onlytwo disulfides are less stable than those with three.

“Variegation” is semirandom mutagenesis of a binding protein. It givesrise to a library of different but structurally related potentialbinding proteins. The residues affected (“variable residues”) arepredetermined, and, in a given round of variegation, are fewer than allof the residues of the protein. At each variable residue position, theallowable “substitution set” is also predetermined, independently, foreach variable residue. It may be anywhere from 2 to 20 different aminoacids, which usually, but need not, include the “wild type” amino acidfor that position. Finally, the relative probabilities with which thedifferent amino acids of the substitution set are expected (based on thesynthetic strategy) to occur at the position are predetermined.

Variegation of a protein is typically achieved by preparing acorrespondingly variegated mixture of DNA (with variable codons encodingvariable residues), cloning it into suitable vectors, and expressing theDNA in suitable host cells.

For any given protein molecule of the library, the choice of amino acidat each variable residue, subject to the above constraints, is random,the result of the happenstance of which DNA expressed that proteinmolecule.

Applicants have screened a large library of LACI (K1) mutants, with thefollowing results:

BPTI # (Lac I) Library Residues Preferred Residues 13 P LHPR HP 16 A AGAG 17 I FYLHINASCPRTVDG NSA 18 M all HL 19 K LWQMKAGSPRTVE QLP 31 E EQ E32 E EQ EQ 34 I all STI 39 E all GEA

In the table above, “library residues” are those permitted to occur,randomly, at that position, in the library, and “preferred residues” arethose appearing at that position in at least one of the 10 variantsidentified as binding to human kallikrein.

At residues 13, 16, 17, 18, 31, and 32, the selections are very strong.At position 34, the selection for either SER or THR is quite strong. Atposition 39, the selection for GLY is strong. Position 19 seems to berather tolerant.

The amino acid residues of the binding proteins of the present inventionmay be, characterized as follows (note that the residues are numbered tocorrespond to BPTI):

(a) the residues involved in disulfide bond formation (C5-C55, C14-C38,and C30-C51);

(b) the residues subjected to variation in the library (13, 16, 17, 18,19, 31, 32, 34, 39); and

(c) the remaining residues.

At a minimum, the Kunitz domain proteins of the present invention mustcontain at least two disulfide bonds, at the same (or nearly the same)positions as in LACI(K1) (residues 50-107 of SEQ ID NO:25). The C₅-C₅₅disulfide is the most important, then the C30-C51, and lastly theC14-C38. If a Cys is replaced, it is preferably a conservativenon-proline substitution with Ala, and Thr especially preferred.

Preferably, three disulfide bonds are formed, at the same, or nearly thesame, positions as in LACI(K₁)(residues 50-107 of SEQ ID NO:25). By“nearly the same”, we mean that as a result of a double mutation, thelocation of a Cys could be shifted by one or two positions along thechain, e.g., Cys30 Gly/Glx31 Cys.

With regard to the variable residues of the library, it should beappreciated that Applicants have not necessarily sequenced all of thepositive mutants in the library, that some of the possible mutantproteins may not actually have been present in the library in detectableamounts, and that, at some-positions, only some of the possible aminoacids were intended to be included in the library. Therefore, theproteins of the present invention, may, at the aforementioned positions(13, 16-19, 31, 32, 34, 39) in decreasing order of preference, exhibit:

(a) the residues specifically identified as preferred;

(b) conservative (or semi-conservative) substitutions for the residuesof (a) above, which were not listed as “library residues”;

(c) nonconservative substitutions for the residues of (a) above, whichwere not listed as library residues;

(d) conservative substitutions for the residues of (a) above, which werelisted as library residues

In addition, for the protein to be substantially homologous withLACI(K1) (residues 50-107 of SEQ ID NO:25), residue 12 must be Gly,residue 23 must be aromatic, residue 33 must be aromatic, residue 37must be Gly, (if the 14-28 disulfide bond is preserved, but otherwise isnot restricted), and residue 45 must be aromatic.

With regard to the remaining residues, these may be, in decreasing orderof preference:

(a) the wild-type amino acid found at that position in LACI (K1)(residues 50-107 of SEQ ID NO:25);

(b) conservative substitutions for (a) above which are also found atthat position in one or more of the homologues of BPTI, or in BPTIitself (SEQ ID NO:1), as listed in Table 15 of the '409 patent;

(c) conservative substitutions for (a) above which are not listed atthat position in Table 15 of the '409 patent;

(d) other amino acids listed at that position in Table 15 of the ‘409patent’

(e) conservative substitutions for the amino acids of (a) above, notalready included in (a)-(c);

(f) any other residues, with non-proline residues being preferred.

Additional variegation could give rise to proteins having higheraffinity for pKA. The intention is to make a new first loop (residues10-21) including what we got in the first variation. Table 202 showsvariegation for residues 10-21. Above the DNA sequence, underscored AAsare from the selected kallikrein binders while bold AAs are those foundin LACI-K1 (residues 50-107 of SEQ ID NO:25). We allow D, E, N, or K at10 (underscored amino acids have been seen on Kunitz domains at position10). We allow 8 AAs at 11: {N, S, I, T, A, G, D, V}. Previousvariegation had allowed {P, L, H, R} at 13. We selected H very strongly;LACI-K1 (residues 50-107 of SEQ ID NO:25) has P at 13 and no reportedKunitz domain has HIS at 13. In one case, PRO was selected at 13.Judging that PRO₁₃ is not optimal, we now allow {E, K, D, Y, Q, H, N}.At 15, we allow K or R. Enzymes that cut after basic residues (K or R)can show two fold tighter binding when the preferred basic residues isavailable. Which is preferred for a given enzyme may well depend on theother residues in the inhibitor; we will allow both. At 16, we add V orD to the group {A, G} previously allowed. LACI-K1 (residues 50-107 ofSEQ ID NO:25) has a hydrophobic residue at 17, but we selected Nstrongly with S allowed (both are hydrophilic). Thus, we allow either Nor S. At 18, we selected HIS strongly with LEU being allowed. We nowallow either HIS or LEU. At 19, we allow eleven amino acids: {A, T, S,P, H, N, Y, Q, K, D, E}. HIS, TYR, ASN, and ASP were not allowed in thefirst variegation. This variegation allows 131,072 DNA sequences and78,848 amino acid sequences; 99.92% of the amino-acid sequences are new.One preferred procedure is to ligate DNA that embodies this variegationinto DNA obtained from selection after the initial variegation atresidues 31, 32, 34, and 39. Thus a small population of sequences atthese locations is combined with the new variegation to produce apopulation of perhaps 10⁷ different sequences. These are then selectedfor binding to human pKA.

A second variegation, shown in Table 204; allows changes at residues 31,32, 34, 39, 40, 41, and 42. In the first selection, we saw strongselection at positions 31 and 32 and weaker selection at positions 34and 39. Thus, we now allow more variability at 31 and 32, lessvariability at 34 and 39, and binary variability at 40, 41, and 42. Thisvariegation allows 131,072 DNA sequences and 70,304 amino-acidsequences. The fraction of amino-acid sequences that are new is 0.997.

The term “substantially homologous”, when used in connection with aminoacid sequences, refers to sequences which are substantially identical toor similar in sequence, giving rise to a homology in conformation andthus to similar biological activity. The term is not intended to imply acommon evolution of the sequences.

Typically, “substantially homologous” sequences are at least 50%, morepreferably at least 80%, identical in sequence, at least over anyregions known to be involved in the desired activity. Most preferably,no more than five residues, other than at the termini, are different.Preferably, the divergence in sequence, at least in the aforementionedregions, is in the form of “conservative modifications”.

“Conservative modifications” are defined as

(a) conservative substitutions of amino acids as hereafter defined; and

(b) single or multiple insertions or deletions of amino acids at thetermini, at interdomain boundaries, in loops or in other segments ofrelatively high mobility (as indicated, e.g., by the failure to clearlyresolve their structure upon X-ray diffraction analysis or NMR).

-   -   Preferably, except at the termini, no more than about five amino        acids are inserted or deleted at a particular locus, and the        modifications are outside regions known to contain binding sites        important to activity.

Conservative substitutions are herein defined as exchanges within one ofthe following five groups:

I. Small aliphatic, nonpolar or slightly polar residues:

-   -   Ala, Ser, Thr (Pro, Gly)

II. Polar, negatively charged residues: and their amides

-   -   Asp, Asn, Glu, Gln

III. Polar, positively charged residues:

-   -   His, Arg, Lys

IV. Large, aliphatic, nonpolar residues:

-   -   Met, Leu, Ile, Val (Cys)

V. Large, aromatic residues:

-   -   Phe, Tyr, Trp

Residues Pro, Gly and Cys are parenthesized because they have specialconformational roles. Cys participates in formation of disulfide bonds.Gly imparts flexibility to the chain. Pro imparts rigidity to the chainand disrupts α helices. These residues may be essential in certainregions of the polypeptide, but substitutable elsewhere.

Semi-conservative substitutions are defined to be exchanges between twoof groups (I)-(V) above which are limited to supergroup (a), comprising(I), (II) and (I) above, or to supergroup (B), comprising (IV) and (V)above.

Two regulatory DNA sequences (e.g., promoters) are “substantiallyhomologous” if they have substantially the same regulatory effect as aresult of a substantial identity in nucleotide sequence. Typically,“substantially homologous” sequences are at least 50%, more preferablyat least 80%, identical, at least in regions known to be involved in thedesired regulation. Most preferably, no more than five bases aredifferent.

The Kunitz domains are quite small; if this should cause apharmacological problem, such as excessively quick elimination from thecirculation, two or more such domains may be joined by a linker. Thislinker is preferably a sequence of one or more amino acids. A preferredlinker is one found between repeated domains of a human protein,especially the linkers found in human BPTI homologues, one of which hastwo domains (BALD85, ALBR83b) and another of which three (WUNT88).Peptide linkers have the advantage that the entire protein may then beexpressed by recombinant DNA techniques. It is also possible to use anonpeptidyl linker, such as one of those commonly used to formimmunogenic conjugates. For example, a BPTI-like KuDom topolyethyleneglycol, so called PEGylation (DAV179).

Certain plasma kallikrein-inhibiting Kunitz domains are shown in Table103. The residues that are probably most important in binding to plasmakallikrein are H₁₃, C₁₄, K15, A₁₆, N₁₇, H₁₈, Q₁₉, E₃₁, E₃₂, and X₃₄(where X is SER or THR). A molecule that presents the side groups ofN₁₇, H₁₈, and Q₁₉ plus any two of the residues H₁₃, C₁₄, K15, (or R₁₅),E₃₁, E₃₂, and X₃₄ (X=SER or THR) in the corresponding orientation islikely to show strong, specific binding for plasma kallikrein. A basicresidue at 15 is NOT thought to be essential.

The compounds are not limited to the side groups found in geneticallyencoded amino acids; rather, conservative substitutions are allowed.LYS₁₅ can be replaced by ARG, ornithine, guanidolysine, and other sidegroups that carry a positive charge. ASN₁₇ can be replaced by othersmall, neutral, hydrophilic groups, such as (but without limitation)SER, O-methyl serine, GLN, α-amidoglycine, ALA, α-aminobutyric acid, andα-amino-γ-hydroxybutyric acid (homoserine). HIS₁₈ could be replaced withother amino acids having one or more of the properties: amphoteric,aromatic, hydrophobic, and cyclic. For example (without limitation),HIS₁₈ could be replaced with L-C^(δ)methylhistidine,L-C^(ε)methylhistidine, L-p-aminophenylalanine,L-m-(N,Ndimethylamino)phenylalanine, canavanine (Merck Index 1745), andN-methylasparagine.

A molecule that presents side groups corresponding to, for example, K15,N₁₇, H₁₈, and E₃₂ might bind to plasma kallikrein in a way that blocksaccess of macromolecules to the catalytic site, even though thecatalytic site is accessible to small molecules. Thus, in testingpossible inhibitors, it is preferred that they be tested againstmacromolecular substrates.

Ways to Improve Specificity of, for Example, KKII/3#7 for PlasmaKallikrein:

Note that K15 or (R₁₅) may not be essential for specific bindingalthough it may be used. Not having a basic residue at the P1 positionmay give rise to greater specificity. The variant KKII/3#7-K15A (SEQ IDNO:31; shown in Table 1017), having an ALA at P1, is likely to be a goodplasma kallikrein inhibitor and may have higher specificity for plasmakallikrein relative to other proteases than does NS4. The affinity ofKKII/3#7-K15A (SEQ ID NO:31) for plasma kallikrein may be less than theaffinity of KKII/3#7 (SEQ ID NO:8) for plasma kallikrein, but in manyapplications, specificity is more important.

Smaller Domains that Bind Plasma Kallikrein:

Kunitz domains contain 58 amino acids (typically). It is possible todesign smaller domains that would have specific binding for plasmakallikrein. Table 50 shows places in BPTI where side groups are arrangedin such a way that a disulfide is likely to form if the existing sidegroups are changed to cysteine. Table 55 shows some “cut-down” domainsthat are expected to bind and inhibit plasma kallikrein.

The first shortened molecule (ShpKa#1, SEQ ID NO:17) is derived fromBPTI and comprises residues 13-39. The mutations P13H, R17N, I18H, I19Q,Q31E, T32E, V34S, and R39G are introduced to increase specific bindingto plasma kallikrein. The mutation Y21C is introduced on the expectationthat a disulfide will form between CYS₂₁ and CYS₃₀. It is also expectedthat a disulfide will form between CYS₁₄ and CYS₃₈ as in BPTI. Thesedisulfides will cause the residues 13-19 and 31-39 to spend most oftheir time in a conformation highly similar to that found for thecorresponding residues of BPTI. This, in turn, will cause the domain tohave a high affinity for plasma kallikrein.

The second shortened molecule (ShpKa#2, SEQ ID NO: 18) is also derivedfrom BPTI and comprises residues 13-52. The mutations P13H, R17N, I18H,I19Q, Q31E, T32E, V34T, and R39G are introduced to increase specificbinding to plasma kallikrein. Because residues 13-52 are included, thetwo natural disulfides 14:38 and 30:51 can form.

A third shortened BPTI derivative (ShpKa#3, SEQ ID NO:19) is similar toShpKa#2 (SEQ ID NO:18) but has the mutations P13H, K15R, R17N, I18H,I19Q, R20C, Q31E, T32E, V34S; Y35C, and R39G. The residues 20 and 35 areclose enough in BPTI that a disulfide could form when both are convertedto cysteine. At position 34, both ASP and GLY seen to give good plasmakallikrein binders. As we are introducing a new disulfide bond between35 and 20, it seems appropriate to allow extra flexibility at 34 byusing SER.

The fourth shortened molecule (ShpKa#4, SEQ ID NO:20) is derived fromthe LACI-K1 derivative KKII/3#7 (residues 13-39 OF SEQ ID NO:8) andcarries only the mutation F21C. It is likely that a disulfide will formbetween CYS₂₁ and CYS₃₀.

ShpKa#5 (SEQ ID NO:21) is related to ShpKa#4 (SEQ ID NO:20) by replacingresidues ILE₂₅-PHE₂₆ with a single GLY. The α carbons of residues 24 and27 are separated by 5.5 Å and this gap can be bridged by a single GLY.

ShpKa#6 (SEQ ID NO:22) is related to ShpKa#4 (SEQ ID NO:20) by theadditional mutations R20C and Y35C. These residues are close in space sothat a third disulfide might form between these residues.

ShpKa#7 (SEQ ID NO:23) is related to ShpKa#6 (SEQ ID NO:22) by themutations N24D, 125V, F26T, and T27E. The subsequence D₂₄ VTE is foundin several Kunitz Domains and reduces the positive charge on themolecule.

ShpKa#8 (SEQ ID NO:24) is related to ShpKa#6 (SEQ ID NO:22) by themutations I25P, F26D, and T27A. The subsequence P₂₅ DA is found in theKuDom of D. funebris. This has the advantage of inserting a proline andreducing net positive charge. It is not known that reduced positivecharge will result in greater affinity or specificity. The ability tochange the charge at a site far from the binding site is an advantage.

Non-Kunitz Domain Inhibitors of Plasma Kallikrein Derived from theLACI-K1 Plasma Kallikrein Inhibitors

The Kunitz domain binding proteins of the present invention can be usedas structural probes of human plasma kallikrein so that smaller protein,small peptidyl, and non-peptidyl drugs may be designed to have highspecificity for plasma kallikrein.

The non-Kunitz domain inhibitors of the present invention can be dividedinto several groups:

-   1) peptides of four to nine residues,-   2) cyclic peptides of five to twenty-five residues,    -   a) those closed by disulfides,    -   b) those closed by main-chain peptide bonds,    -   c) those closed by bonds (other than disulfides) between side        groups,-   3) compounds in which one or more peptide bonds are replaced by    nonpeptidyl bonds which, nonetheless, are somewhat analogous to    peptide bonds in length, structure, etc., so-called    “pseudopeptides”, and-   4) compounds in which the side groups corresponding to those of a    protein are supported by a framework that is not related to peptides    or pseudopeptides.

Inhibitors may belong to more than one of these groups. For example, acompound may be cyclic and have two peptide linkages replaced by“pseudopeptide” linkages, or a compound could have three side groupsattached to an organic ring compound with a dipeptide group alsoattached.

1) Peptides of Four to Nine Residues:

One class of potential inhibitors of plasma kallikrein is peptides offour to nine residues. The peptides are not limited to those composed ofthe genetically-encodable twenty amino acids. Unless stated otherwise,the levo enantiomer (I-or L-) of chiral amino acids (that is, theconformation about the α carbon is as in naturally occurringgenetically-encoded amino acids) is preferred. Peptides of four to nineresidues having the sequence of Formula I are likely to be specificplasma kallikrein inhibitors.X₁—X₂—X₃—X₄—X₅—X₆—X₇—X₈—X₉  Formula 1wherein:

-   —the first residue may be any one of X₁, X₂, X₃, X₄, or X₅; the last    residue may be either X₈ or X₉,-   X₁ corresponds to the P4 residue the inhibitor and may be picked    from the set comprising {any d or l amino acid (having free or    blocked amino group) or an amino group (possibly blocked with one of    the groups acetyl, formyl, methyl, ethyl, propyl, isopropyl,    n-butyl, secondary butyl, tertiary butyl, benzyl, or similar    group)}; preferred choices are hydrogen, acetyl, glycine, and    formyl,-   X₂ corresponds to the P3 residue and is most preferably l-HIS;    alternatives include (without limitation) L-C^(δ)methylhistidine,    L-C^(ε)methylhistidine, L-p-aminophenylalanine,    L-p-(N,Ndimethylamino)phenylalanine, canavanine (Merck Index 1745),    and N-methylasparagine; all the alternatives have one or more of the    properties: amphoteric, aromatic, hydrophobic, and cyclic, as does    HIS,-   X₃ corresponds to the P2 residue and may be any l amino acid,    preferably uncharged and hydrophobic; if X₃ is cysteine, the sulphur    is blocked by one of a) a second cysteine residue, b) a thiol    reagent, c) an alkyl group, if X₃ is not cysteine, then PRO is a    preferred choice because the φ of CYS₁₄ is in the range accessible    to PRO and the side group of PRO is not dissimilar to the disulfide    group, other preferred alternatives at X₃ include l-MET, l-GLN,    l-pipecolic acid (Merck Index 7425), l-2-azitidinecarboxylic acid    (Merck Index 923), l-LEU, l-ILE, l-VAL, cycloleucine (Merck Index    2740), l-α-aminobutyric acid, l-aminocyclopropane-1-carboxylic acid,    and l-methoxyalanine,-   X₄ corresponds to the P1 residue and is most preferably l-LYS,    l-ARG, l-ornithine, or l-guanidolysine (i.e.    NH₂—CH(COOH)—(CH₂)—NH—C—(NH₂)₂ ⁺); l-ALA, l-SER, and GLY are    preferred alternatives,-   X₅ corresponds to the P1′ residue and is most preferably ALA if X₄    is present; 1-PRO, GLY, and 1-SER are preferred alternatives; X₅ may    be any amino acid if X₁-X₄ are absent,-   X₆ corresponds to the P2′ residue and is most preferably l-ASN,    l-SER, l-GLN; other amino acids having small, neutral, hydrophilic    groups; such as (but without limitation) O-methyl serine,    α-amidoglycine, α-aminobutyric acid, β-fluoroalanine,    N-methylasparagine, N,N-dimethylasparagine, and    α-amino-γ-hydroxybutyric acid (homoserine), are preferred    alternatives,-   X₇ corresponds to the P3′ residue and is most preferably HIS;    preferred alternatives include, for example and without limitation,    L-C^(δ)methylhistidine, L-C^(ε)methylhistidine,    L-aminophenylalanine, L-m-(N,Ndimethylamino)phenylalanine,    canavanine (Merck Index 1745), and N-methylasparagine; all the    alternatives have one or more of the properties: amphoteric,    aromatic, hydrophobic, and cyclic, as does HIS,-   X₈ corresponds to the P4′ residue and most preferably is GLN; other    neutral residues including, for example and without limitation, ASN,    α-amino-δ-amidoadipic acid, HIS, and α-amino-ε-amidopimelic acid.    The preferred alternative all have minimal size and no charged    groups, and-   X₉ corresponds to the p5′ residue and may be any l-or d-amino acid,    preferably l-ARG, l-LEU, or l-ALA (which occur frequently at this    position of Kunitz Domains), or GLU, ASP, or other amino acids    having acidic side groups (which might interact with plasma    kallikrein in place of GLU₃₂ or GLU₃₁), or homoserine or other amino    acid having a hydroxyl, or X₉ may be a free or blocked carboxyl    group of X₈ or X₉ may be a free or blocked amide group of X₈; if X₅    is the first amino acid, then X₉ is present.    These compounds can be synthesized by standard solid-phase peptide    synthesis (SPPS) using tBoc or Fmoc chemistry. Synthesis in solution    is also allowed. There are many references to SPPS, including    Synthetic Peptides, Edited by Gregory A Grant, WH Freeman and    Company, New York, 1992, hereinafter GRAN92.

Examples of class 1 include:

-   1.1) +NH₂-GLY₁-HIS-PRO-LYS₄-ALA₅-ASN-HIS-GLN-LEU₉-NH₂ (SEQ ID NO:34;    9 amino acids),-   1.2) +NH₂—HIS-PRO₃-ARG₄-ALA-ASN-HIS-GLN₈-COO— (SEQ ID NO:35; 7 amino    acids),-   1.3) +NH₂—PRO₃-ARG₄-ALA-ASN-HIS₇-COOC2H5 (SEQ ID NO:36; 5 amino    acids),-   1.4) CH₃CO—NH—CH₂—CO-HIS-MET-LYS₄-ALA-ASN-HIS-GLN-GLU-COO— (SEQ ID    NO:37; X₁ is acetylglycine, 9 amino acids),-   1.5) l-pipecolyl-l-orithinyl₄-ALA₅-ASN-L-C^(δ)methylhistidyl-GLN-NH₂    (6 amino acids), and-   1.6)    l-2-azitidinyl-l-guanidolysyl₄-PRO-ASN-HIS-l-α-aminopimelamideyl-GLU-CONH₂    (7 amino acids).    2) Cyclic Peptides of from about 8 to about 25 Amino Acids:

A second class of likely plasma kallikrein inhibitors are cyclicpeptides of from about 8 to about 25 residues in which Formula 1 isextended to allow cyclization between X₈ or X₉ and one of: 1) X₁, 2) X₂,3) X₃, 4) X₄, 5) X₅, or 6) the side group of one of these residues. Theamino acids of this class are not restricted to the twenty geneticallyencodable amino acids. Closure to the amino terminus of residues incases 1-5 involves standard peptide chemistry. Leatherbarrow andSalacinski (LEAT91) report “design of a small peptide-based proteinaseinhibitor by modeling the active-site region of barley chymotrypsininhibitor 2.” This twenty-amino-acid peptide has a K_(D) forchymotrypsin of 28 pM. If the side group of X₃ contains a free thiol, asin CYS, then the peptide may be extended to include a second CYS thatwill form a disulfide with CYS₃. Thus, the sequences of the Formulae 2.1through 2.12 are likely to be specific inhibitors of plasma kallikrein.

Wherein:

-   — the first residue may be any one of X₁, X₂, or X₃,-   X₁ corresponds to the P4 residue the inhibitor and may be picked    from the set comprising {any d or l amino acid (having free or    blocked amino group) or an amino group (possibly blocked with one of    the groups acetyl, formyl, methyl, ethyl, propyl, isopropyl,    n-butyl, secondary butyl, tertiary butyl, benzyl, or similar    group)}; preferred choices are hydrogen, acetyl, glycine, and    formyl,-   X₂ corresponds to the P3 residue and is most preferably l-HIS;    alternatives include (without limitation) L-C^(δ)methylhistidine,    L-C^(ε)methylhistidine, L-p-aminophenylalanine,    L-m-(N,Ndimethylamino)phenylalanine, canavanine (Merck Index 1745),    and N-methylasparagine; all the alternatives have one or more of the    properties: amphoteric, aromatic, hydrophobic, and cyclic, as does    HIS,-   X₃ corresponds to the P2 residue and may be any I amino acid,    preferably uncharged and hydrophobic; if X₃ is cysteine, the sulphur    is blocked by one of a) a second cysteine residue, b) a thiol    reagent, c) an alkyl group, if X₃ is not cysteine, then PRO is a    preferred choice because the φ of CYS₁₄ is in the range accessible    to PRO and the side group of PRO is not dissimilar to the disulfide    group, other preferred alternatives at X₃ include l-MET, l-GLN,    l-pipecolic acid (Merck Index 7425), l-2-azitidinecarboxylic acid    (Merck Index 923), l-LEU, l-ILE, l-VAL, cycloleucine (Merck Index    2740), l-α-aminobutyric acid, l-aminocyclopropane-l-carboxylic acid,    and l-methoxyalanine,-   X₄ corresponds to the P1 residue and is most preferably l-LYS,    l-ARG, l-ornithine, or l-guanidolysine (i.e. NH₂—CH(COOH)—    (CH₂)₄—NH—C—(NH₂)₂+); l-ALA, l-SER, and GLY are preferred    alternatives,-   X₅ corresponds to the P1′ residue and is most preferably ALA if X₄    is present; l-PRO, GLY, and l-SER are preferred alternatives; X₅ may    be any amino acid if X₁-X₄ are absent,-   X₆ corresponds to the P2′ residue and is most preferably l-ASN,    l-SER, l-GLN; other amino acids having small, neutral, hydrophilic    groups, such as (but without limitation) O-methyl serine,    α-amidoglycine, α-aminobutyric acid, β-fluoroalanine,    N-methylasparagine, N,N-dimethylasparagine; and    α-amino-γ-hydroxybutyric acid (homoserine), are preferred    alternatives,-   X₇ corresponds to the P3′ residue and is most preferably HIS;    preferred alternatives include, for example and without limitation,    L-C^(δ)methylhistidine, L-C^(ε)methylhistidine,    L-p-aminophenylalanine, L-m-(N,Ndimethylamino)phenylalanine,    canavanine (Merck Index 1745), and N-methylasparagine; all the    alternatives have one or more of the properties: amphoteric,    aromatic, hydrophobic, and cyclic, as does HIS,-   X₈ corresponds to the P4′ residue and most preferably is GLN; other    neutral residues including, for example and without limitation, ASN,    α-amino-δ-amidoadipic acid, HIS, and α-amino-ε-amidopimelic acid.    The preferred alternative all have minimal size and no charged    groups, and-   X₉ corresponds to the p5′ residue and may be any l-or d-amino acid,    preferably l-ARG, l-LEU, or l-ALA (which occur frequently at this    position of Kunitz Domains), or GLU, ASP, or other amino acids    having acidic side groups (which might interact with plasma    kallikrein in place of GLU₃₂ or GLU₃₁), or homoserine or other amino    acid having a hydroxyl, or X₉ may be a free or blocked carboxyl    group of X₈ or X₉ may be a free or blocked amide group of X₈; if X₅    is the first amino acid, then X₉ is present,-   Linkage is a collection of atoms that connect one of X₈ or    X_(9 to one of X) ₁, X₂, or X₃. The linkage could be closed by any    one or more of disulfide bonds, peptide bonds, other covalent bonds.    The linkage is designed to bend sharply after the recognition    sequence; sequences such as GLY-PRO, PRO-GLY, GLY-GLY, SER-GLY, and    GLY-THR which, are known to favor turns are preferred after the    recognition sequence (X₄-X₈) and (for those cases in which the loop    is closed by main-chain peptide bonds) before the lowest-numbered    residue of Formula 2; the linkage could be picked from the set    comprising:-   1) —(CH₂)_(n)— where n is between 1 and about 18;-   2) —CH₂—(O—CH₂—CH₂)_(n)— where n is between 1 and about 6;-   3) saccharides comprising one to about five hexose, pentose, or    other rings, sugars offering the advantage of favoring solubility;-   4) diaminoepindolidione, 2,6-diaminonaphthylene,    2,6-diaminoanthracene, and similar rigid diamines joined to the    carboxylic acid groups either at the C-terminus or in the side    groups of ASP, GLU, or other synthetic amino acids;-   5) 2,6-dicarboxynaphthylene, 2,6-dicarboxyanthracene, and similar    rigid dicarboxylic acids joined to primary amino groups on the    peptide, such as the α amino group or the side groups of LYS or    ornithine;-   6) one or more benzene, naphthylene, or anthracene-rings or their    heterocyclic analogues, having acidic, oxymethyl, basic, halo, or    nitro side groups and joined through alkyl or ether linkages.

The linker should not be too hydrophobic, especially if it is flexible.A chain of methylene groups is likely to undergo “hydrophobic collapse”(Dan Rich paper.) Ether linkages are chemically stable and avoid thetendency for the linker to collapse into a compact mass.

Some examples, without limitation, of Formula 2 are:

In Formula 2.1, X₂ is an amino group, X₂ is HIS, X₃ is CYS, X₄ is LYS,X₉ is GLU, and the linker is -THR-ILE-THR-THR-CYS-NH₂. The loop isclosed by a disulfide. Table 220 contains the distances between αcarbons of the residues 11 through 21 and 32, 32, and 34 in BPTI. CYS₃in Formula 2.1 corresponds to CYS₁₄ of BPTI and GLU₉ corresponds toARG₂₀. These residues are separated (in the desired conformation) by14.2 Å. Thus the five residue linker can span this gap. The use of THRand ILE favors an extended conformation of the linker. GLU₉ is intendedto interact with the components of plasma kallikrein that interact withGLU₃₁ and GLU₃₂ in the Kunitz-domain KKII/3#7 (SEQ ID NO:8) plasmakallikrein inhibitor.

In Formula 2.2, X₁ is an acetate group, X₃ is CYS, X₄ is ARG, X₉ is GLU,and the linker is -GLU₁₀-THR-THR-VAL-THR-GLY-CYS-NH₂. The loop is closedby a disulfide. This differs from 2.1 in having two acidic residueswhere the chain is likely to turn and where these acidic side groups caninteract with those components of plasma kallikrein that interact withGLU₃₁ and GLU₃₂ in the Kunitz-domain KKII/3#7 (SEQ ID NO:8) plasmakallikrein inhibitor.

In Formula 2.3, X₁ is a glycine, X₂ is HIS, X₃ is CYS, X₄ is ARG, X₆ isGLN, X₉ is GLY (actually part of the linker), and the linker is-GLY₉-PRO-THR-GLY-CYS-NH₂.

In Formula 2.4, the loop is closed by a peptide bond between THR₁₄ andHIS₂. The compound may be synthesized starting at any point and thencyclized. X₃ is PRO and X₄ is ARG. The TTVT sequence favors extendedstructure due to the branches at the β carbons of the side groups. GLY₉favors a turn at that point. GLU₁₀ allows interaction with thosecomponents of plasma kallikrein that interact with GLU₃₁ and GLU₃₂ ofKKII/3#7 (SEQ ID NO:8). GLU₁₀ of formula 2.4 could be replaced withother amino acids having longer acidic side groups such as α-aminoadipicacid or α-aminopimelic acid.

In formulae 2.5, 2.6, and 2.7 there are two disulfides. Having twodisulfides is likely to give the compound greater rigidity and increasethe likelihood that the sequence from 5 to 10 is extended. Having twoconsecutive CYSs favors formation of disulfides to other CYSs,particularly those at the beginning of the peptide. In formula 2.5, thedisulfides are shown from C₂ to C₁₇ and C₄ to C₁₈. This bonding may notbe as favorable to proper conformation of residues 5 through 10 as isthe bonding C₂ to C₁₇ and C₄ to C₁₆ as shown in formula 2.6. Which ofthese forms is probably most strongly influenced by the amino-acidsequence around the cysteines and the buffer conditions in which themolecule folds. Placing charged groups before and after the cysteinesmay favor the desired structure. For example, D₁C₂HC₄K₅ANHQEGPTVD₁₅C₁₆C₁₇K₁₈ (SEQ ID NO:45) would have D₁ close to K₁₈ and K₅close to D₁₅ in the desired structure, but would have D₁ close to D₁5and K₅ close to K₁₈ in the less preferred structure.

Optionally, the side group of X₃ in Formula 2 could be other than CYSbut such that it can selectively form a cross-bridge to a second residuein the chain. As discussed in GRAN92 (p. 141) selective deprotection ofprimary amine and carboxylic acid side groups allows selective formationof intrachain crosslinks.

Formulae 2.8, 2.9, 2.10, and 2.11 show cyclic peptides which are likelyto inhibit plasma kallikrein specifically in which the loop is closed bya peptide bond or bonds between the side groups of amino acids. Duringsynthesis, the substrates for LYS₃ and GLU₁₃ (formula 2.8), GLU₃ andLYS₁₄ (formula 2.9), GLU₂ and GLU₉ (formula 2.10), and LYS₂ and LYS₁₀(formula 2.11) are blocked differently from other reactive side groupsof their respective peptides so that these side groups can bedeprotected while leaving the other groups blocked. The loop is thenclosed and the other side groups deprotected.

The α carbons of LYS and GLU residues that are joined by a peptide bondthrough the side groups may be separated by up to about 8.5 Å. In BPTI(SEQ ID NO: 1), the α carbons of CYS₁₄ and ARG₁₇ are separated by 8.9 Å.The second version of Formula 2.9 shows the peptide chain folded backafter GLY₁₀; PRO₁₁ is approximately as far from the α carbon of residue3 as is the α carbon of GLN₉; THR₁₂ is about as far from residue 3 as isGLN₈; and so forth, so that LYS₁₄ is about as far from residue 3 as isARG₆, which would be about 8.9 Å if the peptide is in the correctconformation. The peptide of formula 2.8 is one amino acid shorter. Thesequence differs by omission of a PRO, so the chain should be lessrigid.

For formula 2.10, the loop is closed by formation of two peptide bondsbetween the side groups of GLU₂ and GLU₉ with 2,6bisaminomethylnaphthylene (FIG. 4, panel E). In Formula 2.11, residues 2and 9 are lysine and 2,6 biscarboxynaphthaylene (FIG. 4, panel D) couldbe used. Linkers of this sort have the advantage that the linker notonly bridges the gap, but that it also keeps the joined amino acidsseparated by at least about 8 Å. This encourages the peptide to foldinto the desired extended conformation.

Loop closure by peptide bond or bonds has the advantage that it is notsensitive to reduction as are disulfides. Unnatural amino acids havedifferent cross-linkable side groups may be used. In particular, acidside groups having more methylene groups, aryl groups, or other groupsare allowed. For example, the side groups —CH₂-p-C₆H₄—COOH,-p-C₆H₄—CH₂—COOH, —(CH₂), —COOH, and -(transCH═CH)—CH₂—COOH could beused. Also, side groups (other than that of LYS) carrying amino groupsmay be used. For example, —(CH₂)₂—NH₃+, —(CH₂)₃—NH₃+, —(CH₂), —NH₃+,—CH₂-2-(6-aminomethylnaphthyl) (shown in FIG. 3, panel A),—CH₂-2-(6-carboxymethylnaphthyl) (shown in FIG. 3, panel B),—CH₂—CH₂-2-(6-aminomethylnaphthyl) (shown in FIG. 3, panel D),—CH₂—CH₁-2-(6-carboxymethylnaphthyl) (shown in FIG. 3, panel E), and—CH₂-p-C₆H₄—CH₂—NH₃+ are suitable.

The naphthylene derivatives shown in FIGS. 3 and 4 have the advantagethat, for the distance spanned, there are relatively few rotatablebonds.

Another alternative within Formula 2 is a repeated cyclic compound: forexample,

Formula 2.12° has two copies of the recognition sequence (HX tandemlyrepeated and cyclized. A GLY is inserted to facilitate a turn.

Let

be an amino-acid analogue that forces a β turn, many of which are knownin the art. Then compounds of formula 2.12 are likely to have thedesired conformation and to show highly specific plasma kallikreinbinding.

Related compounds encompassed in formula 2 include cyclic (PKANHQ

PKANHQ

; SEQ ID NO:50) and cyclic (HMKANHQ

HMKANHQ

; SEQ ID NO:51).

Furthermore, one might increase the specificity to 2.12 by replacing theP1 amino acid (K₄ and K₁₂) with a non-basic amino acid such as ALA, SER,or GLY.

Formula 2.13 embodies two copies of the NHQ subsequence, having the P1′ALA replaced by PRO (to force the appropriate phi angle). Cyclic (ANHQ

ANHQ

; SEQ ID NO:53) is also a likely candidate for specific plasmakallikrein binding.

Also encompassed by formula-2 are compounds like that shown in FIG. 10having the sequence cyclo(bis H-HIS-CYS-LYS-ALA-ASN-HIS-GLN*; SEQ IDNO:54) wherein GLN* is the modified moiety shown and the cycle is closedby two thioether linkages.

Pseudopeptides:

As used herein, a “pseudopeptide” is a linkage that connects two carbonatoms which correspond to the carbons of amino acids and which arecalled the “bridge-head atoms”. The pseudopeptide holds the bridge-headatoms at an appropriate separation, approximately 3.8 Å. Thepseudopeptide is preferably planar, holding the bridge-head atoms in thesame plane as most or all of the atoms of the pseudopeptide. Typically,a pseudopeptide has an amino group and a carboxylic acid group so thatis corresponds roughly to a dipeptide that can be introduced into apeptide by standard Fmoc, tBoc, or other chemistry.

In BPTI, the carbonyl oxygen of K₁₅ projects toward the exterior whilethe amine nitrogen of A₁₆ points toward the interior of BPTI. Thus,pseudopeptides that preserve the carbonyl group are preferred over thosethat do not. Furthermore, pseudopeptides that favor the atomicarrangement found at residues 15 and 16 of Kunitz domains areparticularly favored at residues 15-16 for compounds of the presentinvention. At other positions, pseudopeptides that favor the observedconformation are preferred.

FIGS. 1 and 2 show twelve examples of pseudopeptides; otherpseudopeptides may be used. Of these, ψ1, ψ2, ψ3, ψ5, ψ6, ψ7, ψ8, ψ9,ψ11, and ψ12 maintain the same number of atoms between nominal C_(α)s.ψ4 and ψ10 add an extra atom in the linkage. ψ2, ψ4, ψ6, ψ7, ψ8, ψ9, andψ10 maintain a carbonyl oxygen. ψ1, ψ3, ψ5, can carry electronegativegroups in a place similar to that of the carbonyl oxygen if X₁ is F or—O-alkyl (especially —O—CH₃ or —O—CF₃). The pseudopeptide bond playsseveral roles. First, the pseudopeptide prevents hydrolysis of the bond.To do this, it is usually enough that the bond be stable in water andthat at least one atom of the peptide be changed. It may be sufficientto alkylate the peptide amide. Peptides having PRO at P1′ are oftenhighly resistant to cleavage by serine proteases. A second role of thepseudopeptide if to favor the desired conformation of the residuesjoined by the pseudopeptide. Thirdly, the pseudopeptide provides groupshaving suitable charge; hydrogen-bonding potential, and polarizability.Even so, it must be remembered that only a true peptide will have thesame geometry, charge distribution, and flexibility as a peptide.Changing one atom will alter some property. In most cases, the bindingof the pseudopeptide derivative to the target protease will be lesstight than is the binding of the Kunitz domain from which sequenceinformation was taken. Nevertheless, it is possible that somepseudopeptide derivatives will bind better than true peptides. Tominimize the loss of affinity, it is desirable:

-   -   1) that the pseudopeptide itself be at least roughly planar,    -   2) that the pseudopeptide keep the two joined a carbons in the        plane of the pseudopeptide, and    -   3) that the separation of the two joined a carbons be        approximately 3.8 Å.        ψ1, ψ6, , ψ7, ψ8, and ψ11 are expected to keep the α carbons in        the plane of the pseudopeptide. In ψ8 carbons 1, 2, and 6 plus        the carbonyl O define the plane of the pseudopeptide. ψ8 and ψ9        are likely to be approximately consistent with the geometry        between residues 15 and 16 of a Kunitz domain. The cyclohexone        or cyclohexenone ring does not conflict with groups that are        included in the compounds of the present invention, but would        conflict with atoms of a Kunitz domain.

Kline et al. (KLIN91) have reported use of —CH₂—CO—NH— and —CH₂—NH— inhirulogs that bind plasma kallikrein. DiMaio et al. (DIMA91) havereported using —CO—CH₂— as a pseudopeptide bond in hirulogs that bindplasma kallikrein. Angliker et al. (ANGL87) report synthesis oflysylfluoromethanes and that Ala-Phe-Lys-CH₂F is anactive-centre-directed inhibitor of plasma kallikrein and trypsin.

3) Peptides Having the “Scissile Bond” Replaced by a Pseudopeptide:

A third class of likely plasma kallikrein inhibitors are those in whichsome or all of the peptide bonds are replaced by non-peptide bonds.Groups that replace peptide bonds in compounds derived from peptides areusually referred to as pseudopeptides and designated with the symbol ψ.The most important peptide bond to replace is the one between the P1 andP1′ residues, the so called “scissile bond”. Thus, compounds of theformula 3 or 3a are likely to be specific plasma kallikrein inhibitors.X₁—X₂—X₃—X₄═X₅—X₆—X₇—X₈—X₉  Formula 3:X₁—X₂—X₃—X₄═X₅—X₆═X₇—X₈—X₉  Formula 3awherein:

-   — the first residue may be 1, 2, 3, or 4, and the length of the    compound is at least 5 residues and not more than 9; the —X₄═X₅— and    —X₆═X₇— moieties being counted as two residues,-   X₁ corresponds to the P4 residue the inhibitor and may be picked    from the set comprising {any d or l amino acid (having free or    blocked amino group) or an amino group (possibly blocked with one of    the groups acetyl, formyl, methyl, ethyl, propyl, isopropyl,    n-butyl, secondary butyl, tertiary butyl, benzyl, or similar    group)}; preferred choices are hydrogen, acetyl, glycine, and    formyl,-   X₂ corresponds to the P3 residue and is most preferably l-HIS;    alternatives include (without limitation) L-C^(δ)methylhistidine,    L-C^(ε)methylhistidine, L-p-aminophenylalanine,    L-m-(N,Ndimethylamino)phenylalanine, canavanine (Merck Index 1745),    and N-methylasparagine; all the alternatives have one or more of the    properties: amphoteric, aromatic, hydrophobic, and cyclic, as does    HIS,-   X₃ corresponds to the P2 residue and may be any 1 amino acid,    preferably uncharged and hydrophobic; if X₃ is cysteine, the sulphur    is blocked by one of a) a second cysteine residue, b) a thiol    reagent, c) an alkyl group, if X₃ is not cysteine, then PRO is a    preferred choice because the φ of CYS₁₄ is in the range accessible    to PRO and the side group of PRO is not dissimilar to the disulfide    group, other preferred alternatives at X₃ include l-MET, l-GLN,    l-pipecolic acid (Merck Index 7425), l-2-azitidinecarboxylic acid    (Merck Index 923), l-LEU, l-ILE, l-VAL, cycloleucine (Merck Index    2740), l-α-aminobutyric acid, 1-aminocyclopropane-1-carboxylic acid,    and l-methoxyalanine,-   X₄ corresponds to the P1 residue and is most preferably l-LYS,    l-ARG, l-ornithine, or l-guanidolysine (i.e.    NH₂—CH(COOH)—(CH₂)₄—NH—C—(NH₂)₂+); l-ALA, l-SER, and GLY are    preferred alternatives,-   ═ represents a suitable pseudopeptide that joins the side groups of    X₄ and X₅ and allows the side groups to be in a relative orientation    similar to that found for residues 15 and 16 of Kunitz domains; φ₄    should be approximately −111°, ψ₄ should be approximately 36°, φ₅    should be approximately −80°, ψ₅ should be approximately 164°,-   X₅ corresponds to the P1′ residue and is most preferably ALA if X₄    is present; l-PRO, GLY, and l-SER are preferred alternatives; X₅ may    be any amino acid if X₁-X₄ are absent,-   X₆ corresponds to the P2′ residue and is most preferably l-ASN,    l-SER, l-GLN; other amino acids having small, neutral, hydrophilic    groups, such as (but without limitation) O-methyl serine,    α-amidoglycine, α-aminobutyric acid, β-fluoroalanine,    N-methylasparagine, N,N-dimethylasparagine, and    α-amino-γ-hydroxybutyric acid (homoserine), are preferred    alternatives,-   ═ (if present) is a suitable pseudopeptide that allows the side    groups of X₆ and X₇ to be in a suitable conformation, φ₆ should be    approximately −113°, ψ₆ should be approximately 85°, φ₇ should be    approximately −110°, ψ₇ should be approximately 123°,-   X₇ corresponds to the P3′ residue and is most preferably HIS;    preferred alternatives include, for example and without limitation,    L-C^(δ)methylhistidine, L-C^(ε)methylhistidine,    L-p-aminophenylalanine, L-m-(N,Ndimethylamino)phenylalanine,    canavanine (Merck Index 1745), and N-methylasparagine; all the    alternatives have one or more of the properties: amphoteric,    aromatic, hydrophobic, and cyclic, as does HIS,-   X₈ corresponds to the P4′ residue and most preferably is GLN; other    neutral residues including, for example and without limitation, ASN,    α-amino-δ-amidoadipic acid, HIS, and α-amino-ε-amidopimelic acid.    The preferred alternative all have minimal size and no charged    groups, and-   X₉ corresponds to the p5′ residue and may be any l-or d-amino acid,    preferably l-ARG, l-LEU, or l-ALA (which occur frequently at this    position of Kunitz Domains), or GLU, ASP, or other amino acids    having acidic side groups (which might interact with plasma    kallikrein in place of GLU₃₂ or GLU₃₁), or homoserine or other amino    acid having a hydroxyl, or X₉ may be a free or blocked carboxyl    group of X₈ or X₉ may be a free or blocked amide group of X₈; if X₅    is the first amino acid, then X₉ is present.

The compound VI shown in FIG. 5 can be incorporated in Fmoc synthesis ofpeptides to incorporate —X₄=GLY₅-of formulae 3.1 or 3.2. Other residuetypes can be introduced at residue 5. Compound VI leads to incorporationof ornithine=ALA which can be converted to ARG=ALA withN,N′-di-Cbz-S-methylisothiourea (TIAN92). If Cmpd I contained fourmethylene groups (instead of three), the following synthesis would leadto X₄=LYS. Compounds of the form of formula 3 in which X₄ is ornithineor guanidolysine are likely to be specific inhibitors of plasmakallikrein and should be tested. FIG. 5 shows intermediates involved insynthesis of VI. Compound I is ornithine aldehyde with the α amino groupblocked with Fmoc and the δ amino group blocked with allyloxycarbonyl.The aldehyde can be made by selective reduction of the N^(α)-Fmoc,N^(δ)-Aloc blocked l-ornithine acid (MARC85 p. 397), by reduction of theN^(α)-Fmoc, N^(δ)-Aloc blocked l-ornithine acid chloride (MARC85 p.396), reduction of the N^(α)-Fmoc, N^(δ)-Aloc blocked l-ornithine amide(MARC85 p. 398), or by oxidation of the primary alcohol obtained byreduction of the N^(α)-Fmoc, N^(δ)-Aloc blocked l-ornithine acid withLiAlH₄ (MARC85, p. 1099). Oxidation of the alcohol is carried out withN-bromosuccinimide (MARC85, p. 1057).

Cmpd II is converted to a Grignard reagent and reacted with I; theproduct is III. The free hydrozyl of III is blocked with THP (CARE90, p.678) and the MEM group is removed to give Cmpd IV. Cmpd IV is oxidizedto the carboxylic acid, cmpd V. Cmpd V is then dehydrated to give VI.The synthesis of VI does not guarantee a trans double bond. Thesynthesis of VI given does not lead to a stereospecific product. Thereare chiral centers at carbons 2 and 6. Cmpd VI could, in any event, bepurified by chromatography over an optically active substrate.

Other peptide bonds may be replaced with pseudopeptide bonds.

An option in cmpds of formula 3 is to link the side group of X₃ to thepseudopeptide so as to lock part of the main chain into the correctconformation for binding.

4) Cyclic Peptides Having a Pseudopeptide at the “Scissile Bond”

A fourth class of likely plasma kallikrein inhibitors are those in whichsome or all of the peptide bonds are replaced by non-peptide bonds andthe compound is cyclized. The first peptide bond to replace is the onebetween the P1 and P1′ residues. Thus, compounds of formula 4 or 4a arelikely to be specific inhibitors of plasma kallikrein.

wherein:

-   — the first residue may be 1, 2, 3, or 4, and the length of the    compound is at least 5 residues and not more than 9; the —X₄═X₅— and    —X₆═X₇— moieties being counted as two residues,-   X₁ corresponds to the P4 residue the inhibitor and may be picked    from the set comprising {any d or l amino acid (having free or    blocked amino group) or an amino group (possibly blocked with one of    the groups acetyl, formyl, methyl, ethyl, propyl, isopropyl,    n-butyl, secondary butyl, tertiary butyl, benzyl, or similar    group)}; preferred choices are hydrogen, acetyl, glycine, and    formyl,-   X₂ corresponds to the P3 residue and is most preferably l-HIS;    alternatives include (without limitation) L-C^(δ)methylhistidine,    L-C^(ε)methylhistidine, L-p-aminophenylalanine,    L-m-(N,Ndimethylamino)phenylalanine, canavanine (Merck Index 1745),    and N-methylasparagine; all the alternatives have one or more of the    properties: amphoteric, aromatic, hydrophobic, and cyclic, as does    HIS,-   X₃ corresponds to the P2 residue and may be any l amino acid,    preferably uncharged and hydrophobic; if X₃ is cysteine, the sulphur    is blocked by one of a) a second cysteine residue, b) a thiol    reagent, c) an alkyl group, if X₃ is not cysteine, then PRO is a    preferred choice because the φ of CYS₁₄ is in the range accessible    to PRO and the side group of PRO is not dissimilar to the disulfide    group, other preferred alternatives at X₃ include l-MET, l-GLN,    l-pipecolic acid (Merck Index 7425), l-2-azitidinecarboxylic acid    (Merck Index 923), l-LEU, l-ILE, l-VAL, cycloleucine (Merck Index    2740), l-α-aminobutyric acid, l-aminocyclopropane-l-carboxylic acid,    and l-methoxyalanine,-   X₄ corresponds to the P1 residue and is most preferably l-LYS,    l-ARG, l-ornithine, or l-guanidolysine (i.e.    NH₂—CH(COOH)—(CH₂)₄—NH—C—(NH₂)₂+); l-ALA, l-SER, and GLY are    preferred alternatives,-   ═ represents a suitable pseudopeptide that joins the side groups of    X₄ and X₅ and allows the side groups to be in a relative orientation    similar to that found for residues 15 and 16 of Kunitz domains; φ₄    should be approximately −111°, ψ₄ should be approximately 36°, φ₅    should be approximately −80°, ψ₅ should be approximately 164°,-   X₅ corresponds to the P1′ residue and is most preferably ALA if X₄    is present; l-PRO, GLY, and l-SER are preferred alternatives; X₅ may    be any amino acid if X₁-X₄ are absent,-   X₆ corresponds to the P2′ residue and is most preferably l-ASN,    l-SER, l-GLN; other amino acids having small, neutral, hydrophilic    groups, such as (but without limitation) O-methyl serine,    α-amidoglycine, α-aminobutyric acid, β-fluoroalanine,    N-methylasparagine, N,N-dimethylasparagine, and    α-amino-γ-hydroxybutyric acid (homoserine), are preferred    alternatives,-   ═ (if present) is a suitable pseudopeptide that allows the side    groups of X₆ and X₇ to be in a suitable conformation, φ₆ should be    approximately −113°, ψ₆ should be approximately 85°, φ₇ should be    approximately −110°, ψ₇ should be approximately 123°,-   X₇ corresponds to the P3′ residue and is most preferably HIS;    preferred alternatives include, for example and without limitation,    L-C^(δ)methylhistidine, L-C^(ε)methylhistidine,    L-p-aminophenylalanine, L-m-(N,Ndimethylamino)phenylalanine,    canavanine (Merck Index 1745), and N-methylasparagine; all the    alternatives have one or more of the properties: amphoteric,    aromatic, hydrophobic, and cyclic, as does HIS,-   X₈ corresponds to the P4′ residue and most preferably is GLN; other    neutral residues including, for example and without limitation, ASN,    α-amino-δ-amidoadipic acid, HIS, and α-amino-ε-amidopimelic acid.    The preferred alternative all have minimal size and no charged    groups, and    -   X₉ corresponds to the p5′ residue and may be any l-or d-amino        acid, preferably l-ARG, l-LEU, or l-ALA (which occur frequently        at this position of Kunitz Domains), or GLU, ASP, or other amino        acids having acidic side groups (which might interact with        plasma kallikrein in place of GLU₃₂ or GLU₃₁), or homoserine or        other amino acid having a hydroxyl, or X₉ may be a free or        blocked carboxyl group of X₈ or X₉ may be a free or blocked        amide group of X₈; if X₅ is the first amino acid, then X₉ is        present,-   Linker may be a chain of carbon, nitrogen, oxygen, sulphur,    phosphorus, or other multivalent atoms. In BPTI (Brookhaven Protein    Data Bank entry ITPA), N₁₃ is separated from C₁₉ by 14.6 Å. In    aliphatic groups, carbon atoms are separated by about 1.54 Å and    have bond angles of 109°; thus, an extended chain covers about 1.25    Å per CH₂ group. Accordingly, a chain of about 12 or more methylene    groups would span the gap and allow the partially peptidyl chain to    take up its preferred conformation. Linkers that contain hydrophilic    groups, such as —OH, —NH₂, —COOH, —O—CH₃, may improve solubility.    Linkers that contain aromatic groups (for example paraphenyl or 2,6    naphthylene) are allowed. An alternative is a peptidyl linker.    Peptidyl linkers that are highly resistant to proteolysis are    preferred. The gap of 14.5 Å could be bridged by five or six    residues Thus, sequences such as GPTVG, GPTITG, GPETD, GPTGE,    GTVTGG, DGPTTS or GPDFGS (SEQ ID NOs:55-61, respectively) would be    appropriate. PRO is preferred because it is resistant to    proteolysis. THR, VAL, and ILE are preferred because they favor    extended structure. Charged amino acids (ASP, GLU, LYS, and ARG) are    preferred because they improve solubility. GLY, SER, PRO, ASP, and    ASN are preferred at the ends because they facilitate the needed    turns. For plasma kallikrein binding, acidic groups near the start    of the linker are preferred.

FIG. 9 shows compounds 4.1 and 4.2 according to formula 4. Compound 4.1has a linker consisting of —(CH₂)₁₂—. Although the linker is purelyhydrophobic, compound 4.1 contains residues X₄ (LYS or ARG), ARG₆, andX₈ (ARG or LYS) which are all positively charged. Furthermore, thenitrogen of PRO₂ is not an amide nitrogen, but a secondary or tertiaryamine which would probably be protonated in aqueous solution. Compound4.2 differs from compound 4.1 in that two hydroxyl groups have beenincorporated into the linker to improve solubility.

An option in cmpds of formula 4 is to link the side group of X₃ to thepseudopeptide so as to lock part of the main chain into the correctconformation for binding.

5) Compounds Having at Least Three Side Groups on Non-Peptide Framework:

A fifth class of inhibitors contains the side groups corresponding tothose (using Kunitz domain numbering) of X₁₅ (ARG or LYS), HIS₁₈, ASN₁₇,GLN₁₉, GLU₃₂, GLU₃₁, HIS₁₃, and X₃₄ (X=SER or THR) supported by anon-peptide framework that hold the α carbon at the correct position andcauses the α-β bond to be directed in the correct direction. Inaddition, GLY₁₂ is included, as desired. Furthermore, electronegativeatoms which are hydrogen-bond acceptors are positioned where some or allof the carbonyl oxygens are found in BPTI. In addition, hydrogen-bonddonors are positioned where some or all of the amido nitrogen are foundin BPTI. A minimum number of peptide bonds are included.

In a preferred embodiment, organic compounds (known to be synthesizable)are considered as possible frameworks. Compounds that are fairly rigidare preferred. Compounds not known to give rise to toxic break-downproducts are preferred. Compounds that are reasonably soluble arepreferred, but we are attaching three basic side groups, so thispreference is not strong.

The four side groups thought to comprise the pharmacophore are used tojudge the suitability of each framework. For plasma kallikrein, the sidegroups X₁₅ (ARG, LYS, or other basic amino acid), HIS₁₈, ASN₁₇, GLN₁₉,GLU₃₂, GLU₃₁, HIS₁₃, and X₃₄ (X=SER or THR) in the above formulae aretaken as most important. The relative positions of these groups could bedetermined by X-ray diffraction or NMR. A model based on BPTI may alsobe used. Table 40 shows the coordinates of BPTI.

Wilson et al. (WIL93) describe an algorithm for designing an organicmoiety to substitute or a large segment of a protein and to hold crucialresidues in the appropriate conformation for binding. Compounds of thepresent invention can be designed using the same mathematical algorithm.Where Wilson et al. identify bonds of the peptide backbone and seeksorganic frameworks to hold remaining parts of the parental protein inplace, we identify several bonds leading from the backbone to the sidegroups and replace the backbone with an organic or organometallicframework that holds only side groups or parts of side groups in place.

Mode of Production

The proteins of the present invention may be produced by anyconventional technique, including

(a) nonbiological synthesis by sequential coupling of component aminoacids,

(b) production by recombinant DNA techniques in a suitable host cell,and

(c) removal of undesired sequences from LACI and coupling of syntheticreplacement sequences

The proteins disclosed herein are preferably produced, recombinantly, ina suitable host, such as bacteria from the genera Bacillus, Escherichia,Salmonella, Erwinia, and yeasts from the genera Hansenula,Kluyveromyces, Pichia, Rhinosporidium, Saccharomyces, andSchizosaccharomyces, or cultured mammalian cells such as COS-1. The morepreferred hosts are microorganisms of the species Pichia pastoris,Bacillus subtilis, Bacillus brevis, Saccharomyces cerevisiae,Escherichia coli and Yarrowia lipolytica. Any promoter, regulatable orconstitutive, which is functional in the host may be used to controlgene expression.

Preferably the proteins are secreted. Most preferably, the proteins areobtained from conditioned medium. It is not requited that the proteinsdescribed herein be secreted. Secretion is the preferred route becauseproteins are more likely to fold correctly, can be produced inconditioned medium with few contaminants, and are less likely to betoxic to host cells.

Unless there is a specific reason to include glycogroups, we preferproteins designed to lack N-linked glycosylation sites so that they canbe expressed in a wide variety of organisms including: 1) E. coli, 2) B.subtilis, 3) P. pastoris, 4) S. cerevisiae; and 5) mammalian cells.

Many cells used for engineered secretion of fusion proteins are lessthan optimal because they produce proteases that degrade the fusionprotein. Several means exist for reducing this problem. There arestrains of cells that are deficient in one or another of the offendingproteases; Baneyx and Georgiou (BANE90) report that E. coli OmpT (anouter surface protease) degrades fusion proteins secreted from E. coli.They stated that an OmpT-strain is useful for production of fusionproteins and that degP-and ompT-mutations are additive. Baneyx andGeorgiou (BANE91) report a third genetic locus (ptr) where mutation canimprove the yield of engineered fusions.

Van Dijl et al. (1992) report cloning, expression, and function of B.subtilis signal peptidase (SPase) in E. coli. They found thatoverexpression of the spase gene lead to increased expression of aheterologous fusion protein. Use of strains having augmented secretioncapabilities is preferred.

Anba et al. (1988) found that addition of PMSF to the culture mediumgreatly improved the yield of a fusion of phosphate binding protein(PhoS) to human growth hormone releasing factor (mhGRF).

Other factors that may affect production of these and other proteinsdisclosed herein include: 1) codon usage (it is preferred to optimizethe codon usage for the host to be used), signal sequence, 3) amino-acidsequence at intended processing sites, presence and localization ofprocessing enzymes, deletion, mutation, or inhibition of various enzymesthat might alter or degrade the engineered product and mutations thatmake the host more permissive in secretion (permissive secretion hostsare preferred).

Standard reference works setting forth the general principles ofrecombinant DNA technology include Watson, J. D. et al., MolecularBiology of the Gene, Volumes I and II, The Benjamin/Cummings PublishingCompany, Inc., publisher, Menlo Park, Calif. (1987); Darnell, J. E. etal., Molecular Cell Biology, Scientific American Books, Inc., publisher,New York, N.Y. (1986); Lewin, B. M., Genes II, John Wiley & Sons,publishers, New York, N.Y. (1985); Old, R. W., et al., Principles ofGene Manipulation: An Introduction to Genetic Engineering, 2d edition,University of California Press, publisher, Berkeley, Calif. (1981);Sambrook, J. et al., Molecular Cloning: A Laboratory Manual, Cold SpringHarbor Laboratory, Cold Spring Harbor, N.Y. (1989); and Ausubel et alCurrent Protocols in Molecular Biology, Wiley Interscience, N.Y., (1987,1992). These references are herein entirely incorporated by reference.

Preparation of Peptides

Chemical polypeptide synthesis is a rapidly evolving area in the art,and methods of solid phase polypeptide synthesis are well-described inthe following references, hereby entirely incorporated by reference:(Merrifield, B., J. Amer. Chem. Soc. 85:2149-2154 (1963); Merrifield,B., Science 232:341-347 (1986); Wade, J. D. et al., Biopolymers25:S21-S37 (1986); Fields, G. B., Int. J. Polypeptide Prot. Res. 35:161(1990); MilliGen Report Nos. 2 and 2a, Millipore Corporation, Bedford;MA, 1987) Ausubel et al, supra, and Sambrook et al, supra.

In general, as is known in the art, such methods involve blocking orprotecting reactive functional groups, such as free amino, carboxyl andthio groups. After polypeptide bond formation, the protective groups areremoved (or de-protected). Thus, the addition of each amino acid residuerequires several reaction steps for protecting and deprotecting. Currentmethods utilize solid phase synthesis, wherein the C-terminal amino acidis covalently linked to an insoluble resin particle large enough to beseparated from the fluid phase by filtration. Thus, reactants areremoved by washing the resin particles with appropriate solvents usingan automated programmed machine. The completed polypeptide chain iscleaved from the resin by a reaction which does not affect polypeptidebonds.

In the more classical method, known as the “tBoc method,” the aminogroup of the amino acid being added to the resin-bound C-terminal aminoacid is blocked with tert-butyloxycarbonyl chloride (tBoc). Thisprotected amino acid is reacted with the bound amino acid in thepresence of the condensing agent dicyclohexylcarbodiimide, allowing itscarboxyl group to form a polypeptide bond the free amino group of thebound amino acid. The amino-blocking group is then removed byacidification with trifluoroacetic acid (TFA); it subsequentlydecomposes into gaseous carbon dioxide and isobutylene. These steps arerepeated cyclically for each additional amino acid residue. A morevigorous treatment with hydrogen fluoride (HF) ortrifluoromethanesulfonyl derivatives is common at the end of thesynthesis to cleave the benzyl-derived side chain protecting groups andthe polypeptide-resin bond.

More recently, the preferred “Fmoc” technique has been introduced as analternative synthetic approach, offering milder reaction conditions,simpler activation procedures and compatibility with continuous flowtechniques. This method was used, e.g., to prepare the peptide sequencesdisclosed in the present application. Here, the ∝-amino group isprotected by the base labile 9-fluorenylmethoxycarbonyl (Fmoc) group.The benzyl side chain protecting groups are replaced by the more acidlabile t-butyl derivatives. Repetitive acid treatments are replaced bydeprotection with mild base solutions, e.g., 20% piperidine indimethylformamide (DMF), and the final HF cleavage treatment iseliminated. A TFA solution is used instead to cleave side chainprotecting groups and the polypeptide resin linkage simultaneously.

At least three different polypeptide-resin linkage agents can be used:substituted benzyl alcohol derivatives that can be cleaved with 95% TFAto produce a polypeptide acid, methanolic ammonia to produce apolypeptide amide, or 1% TFA to produce a protected polypeptide whichcan then be used in fragment condensation procedures, as described byAtherton, E. et al., J. Chem. Soc. Perkin Trans. 1:538-546 (1981) andSheppard, R. C. et al., Int. J. Polypeptide Prot. Res. 20:451-454(1982). Furthermore, highly reactive Fmoc amino acids are available aspentafluorophenyl esters or dihydro-oxobenzotriazine esters derivatives,saving the step of activation used in the tBoc method.

Chemical Modification of Amino Acids

Covalent modifications of amino acids contained in proteins of interestare included within the scope of the present invention. Suchmodifications may be introduced into an epitopic peptide and/oralloantigenic peptide by reacting targeted amino acid residues of thepolypeptide with an organic derivatizing agent that is capable ofreacting with selected side chains or terminal residues. The followingexamples of chemical derivatives are provided by way of illustration andnot by way of limitation.

Aromatic amino acids may be replaced with D-or L-naphthylalanine, D-orL-Phenylglycine, D-or L-2-thienylalanine, D-or L-1-, 2-, 3-or4-pyrenylalanine, D-or L-3-thienylalanine, D-or L-(2-pyridinyl)-alanine,D-or L-(3-pyridinyl)-alanine, D-or L-(2-pyrazinyl)-alanine, D-orL-(4-isopropyl)-phenylglycine, D-(trifluoromethyl)-phenylglycine,D-(trifluoromethyl)-phenylalanine, D-p-fluorophenylalanine, D-orL-p-biphenylphenylalanine, D-or L-p-methoxybiphenylphenylalanine, D-orL-2-indole-(alkyl)alanines, and D-or L-alkylalanines where alkyl may besubstituted or unsubstituted methyl, ethyl, propyl, hexyl, butyl,pentyl, iso-propyl, iso-butyl, sec-isotyl, iso-pentyl, non-acidic aminoacids, of C1-C20.

Acidic amino acids can be substituted with non-carboxylate amino acidswhile maintaining a negative charge, and derivatives or analogs thereof,such as the non-limiting examples of (phosphono)-alanine, glycine,leucine, isoleucine, threonine, or serine; or sulfated (e.g., —SO₃H)threonine, serine, tyrosine.

Other substitutions may include unnatural hydroxylated amino acids maymade by combining “alkyl” (as defined and exemplified herein) with anynatural amino acid. Basic amino acids may be substituted with alkylgroups at any position of the naturally occurring amino acids lysine,arginine, ornithine, citrulline, or (guanidino)-acetic acid, or other(guanidino)alkyl-acetic acids, where “alkyl” is define as above. Nitrilederivatives (e.g., containing the CN-moiety in place of COOH) may alsobe substituted for asparagine or glutamine, and methionine sulfoxide maybe substituted for methionine. Methods of preparation of such peptidederivatives are well known to one skilled in the art.

In addition, any amide linkage in any of the proteins can be replaced bya ketomethylene moiety, e.g. (—C(═O)—CH₂—) for (—(C═O)—NH—). Suchderivatives are expected to have the property of increased stability todegradation by enzymes, and therefore possess advantages for theformulation of compounds which may have increased in vivo half lives, asadministered by oral, intravenous, intramuscular, intraperitoneal,topical, rectal, intraocular, or other routes.

In addition, any amino acid representing a component of the saidproteins can be replaced by the same amino acid but of the oppositechirality. Thus, any amino acid naturally occurring in theL-configuration (which may also be referred to as the R or Sconfiguration, depending upon the structure of the chemical entity) maybe replaced with an amino acid of the same chemical structural type, butof the opposite chirality, generally referred to as the D-amino acid butwhich can additionally be referred to as the R-or the S-, depending uponits composition and chemical configuration. Such derivatives have theproperty of greatly increased stability to degradation by enzymes, andtherefore are advantageous in the formulation of compounds which mayhave longer in vivo half lives, when administered by oral, intravenous,intramuscular, intraperitoneal, topical, rectal, intraocular, or otherroutes.

Additional amino acid modifications of amino acids of proteins of thepresent invention may include the following: Cysteinyl residues may bereacted with alpha-haloacetates (and corresponding amines), such as2-chloroacetic acid or chloroacetamide, to give carboxymethyl orcarboxyamidomethyl derivatives. Cysteinyl residues may also bederivatized by reaction with compounds such as bromotrifluoroacetone,alpha-bromo-beta-(5-imidozoyl)propionic acid, chloroacetyl phosphate,N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyldisulfide, p-chloromercuribenzoate, 2-chloromercuri-4-nitrophenol, orchloro-7-nitrobenzo-2-oxa-1,3-diazole.

Histidyl residues may be derivatized by reaction with compounds such asdiethylprocarbonate e.g., at pH 5.5-7.0 because this agent is relativelyspecific for the histidyl side chain, and para-bromophenacyl bromide mayalso be used; e.g., where the reaction is preferably performed in 0.1 Msodium cacodylate at pH 6.0.

Lysinyl and amino terminal residues may be reacted with compounds suchas succinic or other carboxylic acid anhydrides. Derivatization withthese agents is expected to have the effect of reversing the charge ofthe lysinyl residues. Other suitable reagents for derivatizingalpha-amino-containing residues include compounds such asimidoesters/e.g., as methyl picolinimidate; pyridoxal phosphate;pyridoxal; chloroborohydride; trinitrobenzenesulfonic acid;O-methylisourea; 2,4 pentanedione; and transaminase-catalyzed reactionwith glyoxylate., Arginyl residues may be modified by reaction with oneor several conventional reagents, among them phenylglyoxal,2,3-butanedione, 1,2-cyclohexanedione, and ninhydrin according to knownmethod steps. Derivatization of arginine residues requires that thereaction be performed in alkaline conditions because of the high pKa ofthe guanidine functional group. Furthermore, these reagents may reactwith the groups of lysine as well as the arginine epsilon-amino group.

The specific modification of tyrosyl residues per se is well-known, suchas for introducing spectral labels into tyrosyl residues by reactionwith aromatic diazonium compounds or tetranitromethane. N-acetylimidizoland tetranitromethane may be used to form O-acetyl tyrosyl species and3-nitro derivatives, respectively.

Carboxyl side groups (aspartyl or glutamyl) may be selectively-modifiedby reaction with carbodiimides (R′—N—C—N—R′) such asl-cyclohexyl-3-(2-morpholinyl-(4-ethyl) carbodiimide orl-ethyl-3-(4-azonia-4,4-dimethylpentyl) carbodiimide. Furthermore,aspartyl and glutamyl residues may be converted to asparaginyl andglutaminyl residues by reaction with ammonium ions.

Glutaminyl and asparaginyl residues may be frequently deamidated to thecorresponding glutamyl and aspartyl residues. Alternatively, theseresidues may be deamidated under mildly acidic conditions. Either formof these residues falls within the scope of the present invention.

Derivatization with bifunctional agents is useful for cross-linking thepeptide to a water-insoluble support matrix or to other macromolecularcarriers, according to known method steps. Commonly used cross-linkingagents include, e.g., 1,1-bis(diazoacetyl)-2-phenylethane,glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with4-azidosalicylic acid, homobifunctional imidoesters, includingdisuccinimidyl esters such as 3,3′-dithiobis(succinimidylpropionate),and bifunctional maleimides such as bis-N-maleimido-1,8-octane.Derivatizing agents such asmethyl-3-[(p-azidophenyl)dithio]propioimidate yield photoactivatableintermediates that are capable of forming crosslinks in the presence oflight. Alternatively, reactive water-insoluble matrices such as cyanogenbromide-activated carbohydrates and the reactive substrates described inU.S. Pat. Nos. 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537;and 4,330,440 (which are herein incorporated entirely by reference), maybe employed for protein immobilization.

Other modifications of proteins of the present invention may includehydroxylation of proline and lysine, phosphorylation of hydroxyl groupsof seryl or threonyl residues, methylation of the alpha-amino groups oflysine, arginine, and histidine side chains (T. E. Creighton, Proteins:Structure and Molecule Properties. W.H. Freeman & Co., San Francisco,pp. 79-86 (1983)), acetylation of the N-terminal amine, methylation ofmain chain amide residues (or substitution with N-methyl amino acids)and, in some instances, amidation of the C-terminal carboxyl groups,according to known method steps. Glycosylation is also possible.

Such derivatized moieties may improve the solubility, absorption,permeability across the blood brain barrier biological half life, andthe like. Such moieties or modifications of proteins may alternativelyeliminate or attenuate any possible undesirable side effect of theprotein and the like. Moieties capable of mediating such effects aredisclosed, for example, in Remington's Pharmaceutical Sciences, 16thed., Mack Publishing Co., Easton, Pa. (1980).

Such chemical derivatives of proteins also may provide attachment tosolid supports, including but not limited to, agarose, cellulose, hollowfibers, or other polymeric carbohydrates such as agarose, cellulose,such as for purification, generation of antibodies or cloning; or toprovide altered physical properties, such as resistance to enzymaticdegradation or increased antigenic properties, which is desired fortherapeutic compositions comprising proteins of the present invention.Such peptide derivatives are well known in the art, as well as methodsteps for making such derivatives using carbodiimides active esters ofN-hydroxy succinimide, or mixed anhydrides, as non-limiting examples.

Assays for Kallikrein Binding and Inhibition

The proteins may be assayed for kallikrein-binding activity by anyconventional method. Scatchard (Ann NY Acad Sci (1949) 51:660-669)described a classical method of measuring and analyzing binding whichhas been applied to the binding of proteins. This method requiresrelatively pure protein and the ability to distinguish bound proteinfrom unbound.

A second method appropriate for measuring the affinity of inhibitors forenzymes is to measure the ability of the inhibitor to slow the action ofthe enzyme. This method requires, depending on the speed at which theenzyme cleaves substrate and the availability of chromogenic orfluorogenic substrates, tens of micrograms to milligrams of relativelypure inhibitor.

A third method of determining the affinity of a protein for a secondmaterial is to have the protein displayed on a genetic package, such asM13, and measure the ability of the protein to adhere to the immobilized“second material”. This method is highly sensitive because the geneticpackages can be amplified. We obtain at least semiquantitative valuesfor the binding constants by use of a pH step gradient. Inhibitors ofknown affinity for the immobilized protease are used to establishstandard profiles against which other phage-displayed inhibitors arejudged.

Preferably, the proteins of the present invention have a bindingactivity against plasma kallikrein such that the complex has adissociation constant of at most 200 pM, more preferably at most 50 pM.Preferably, their inhibitory activity is sufficiently high so that theKi of binding with plasma kallikrein is less than 500 pM, morepreferably less than 50 pM.

Pharmaceutical Methods and Preparations

The preferred animal subject of the present invention is a mammal. Bythe term “mammal” is meant an individual belonging to the classMammalia. The invention is particularly useful in the treatment of humansubjects, although it is intended for veterinary uses as well.

The term “protection”, as used herein, is intended to include“prevention,” “suppression” and “treatment.” “Prevention” involvesadministration of the protein prior to the induction of the disease.“Suppression” involves administration of the composition prior to theclinical appearance of the disease. “Treatment” involves administrationof the protective composition after the appearance of the disease.

It will be understood that in human and veterinary medicine, it is notalways possible to distinguish between “preventing” and “suppressing”since the ultimate inductive event or events may be unknown, latent, orthe patient is not ascertained until well after the occurrence of theevent or events. Therefore, it is common to use the term “prophylaxis”as distinct from “treatment” to encompass both “preventing” and“suppressing” as defined herein. The term “protection,” as used herein,is meant to include “prophylaxis.” It should also be understood that tobe useful, the protection provided need not be absolute, provided thatit is sufficient to carry clinical value. An agent which providesprotection to a lesser degree than do competitive agents may still be ofvalue if the other agents are ineffective for a particular individual,if it can be used in combination with other agents to enhance the levelof protection, or if it is safer than competitive agents.

At least one of the proteins of the present invention may beadministered, by any means that achieve their intended purpose, toprotect a subject against a disease or other adverse condition. The formof administration may be systemic or topical. For example,administration of such a composition may be by various parenteral routessuch as subcutaneous, intravenous, intradermal, intramuscular,intraperitoneal, intranasal, transdermal, or buccal routes.Alternatively, or concurrently, administration may be by the oral route.Parenteral administration can be by bolus injection or by gradualperfusion over time.

A typical regimen comprises administration of an effective amount of theprotein, administered over a period ranging from a single dose, todosing over a period of hours, days, weeks, months, or years.

It is understood that the suitable dosage of a protein of the presentinvention will be dependent upon the age, sex, health, and weight of therecipient, kind of concurrent treatment, if any, frequency of treatment,and the nature of the effect desired. However, the most preferred dosagecan be tailored to the individual subject, as is understood anddeterminable by one of skill in the art, without undue experimentation.This will typically involve adjustment of a standard dose, e.g.,reduction of the dose if the patient has a low body weight.

Prior to use in humans, a drug will first be evaluated for safety andefficacy in laboratory animals. In human clinical studies, one wouldbegin with a dose expected to be safe in humans, based on thepreclinical data for the drug in question, and on customary doses foranalogous drugs (if any). If this dose is effective, the dosage may bedecreased, to determine the minimum effective dose, if desired. If thisdose is ineffective, it will be cautiously increased, with the patientsmonitored for signs of side effects. See, e.g., Berkow et al, eds., TheMerck Manual. 15th edition, Merck and Co., Rahway, N.J., 1987; Goodmanet al., eds., Goodman and Gilman's The Pharmacological Basis ofTherapeutics, 8th edition, Pergamon Press, Inc., Elmsford, N.Y., (1990);Avery's Drug Treatment: Principles and Practice of Clinical Pharmacologyand Therapeutics, 3rd edition, ADIS Press, LTD., Williams and Wilkins,Baltimore, Md. (1987), Ebadi, Pharmacology, Little, Brown and Co.,Boston, (1985), which references and references cited therein, areentirely incorporated herein by reference.

The total dose required for each treatment may be administered bymultiple doses or in a single dose. The protein may be administeredalone or in conjunction with other therapeutics directed to the diseaseor directed to other symptoms thereof.

The appropriate dosage form will depend on the disease, the protein, andthe mode of administration; possibilities include tablets, capsules,lozenges, dental pastes, suppositories, inhalants, solutions, ointmentsand parenteral depots. See, e.g., Berker, supra, Goodman, supra. Avery,supra and Ebadi, supra, which are entirely incorporated herein byreference, including all references cited therein.

In addition to at least one protein as described herein, apharmaceutical composition may contain suitable pharmaceuticallyacceptable carriers, such as excipients, carriers and/or auxiliarieswhich facilitate processing of the active compounds into preparationswhich can be used pharmaceutically. See, e.g., Berker, supra, Goodman,supra, Avery, supra and Ebadi, supra, which are entirely incorporatedherein by reference, included all references cited therein.

In Vitro Diagnostic Methods and Reagents

The in vitro assays of the present invention may be applied to anysuitable analyte-containing sample, and may be qualitative orquantitative in nature. In order to detect the presence, or measure theamount, of an analyte, the assay must provide for a signal producingsystem (SPS) in which there is a detectable difference in the signalproduced, depending on whether the analyte is present or absent (or, ina quantitative assay, on the amount of the analyte). The detectablesignal may be one which is visually detectable, or one detectable onlywith instruments. Possible signals include production of colored orluminescent products, alteration of the characteristics (includingamplitude or polarization) of absorption or emission of radiation by anassay component or product, and precipitation or agglutination of acomponent or product. The term “signal” is intended to include thediscontinuance of an existing signal, or a change in the rate of changeof an observable parameter, rather than a change in its absolute value.The signal may be monitored manually or automatically.

The component of the signal producing system which is most intimatelyassociated with the diagnostic reagent is called the “label”. A labelmay be, e.g., a radioisotope, a fluorophore, an enzyme, a co-enzyme, anenzyme substrate, an electron-dense compound, an agglutinable particle.

The radioactive isotope can be detected by such means as the use of agamma counter or a scintillation counter or by autoradiography. Isotopeswhich are particularly useful for the purpose of the present inventionare ³H, ¹²⁵I, ¹³¹I, ³⁵S, ¹⁴C, and, preferably, ¹²⁵I.

It is also possible to label a compound with a fluorescent compound.When the fluorescently labeled antibody is exposed to light of theproper wave length, its presence can then be detected due tofluorescence. Among the most commonly used fluorescent labellingcompounds are fluorescein isothiocyanate, rhodamine, phycoerythrin,phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.

Alternatively, fluorescence-emitting metals such as ¹²⁵Eu, or others ofthe lanthanide series, may be attached to the binding protein using suchmetal chelating groups as diethylenetriaminepentaacetic acid (DTPA) ofethylenediamine-tetraacetic acid (EDTA).

The binding proteins also can be detectably labeled by coupling to achemiluminescent compound. The presence of the chemiluminescentlylabeled antibody is then determined by detecting the presence ofluminescence that arises during the course of a chemical reaction.Examples of particularly useful chemiluminescent-labeling compounds areluminol, isoluminol, theromatic acridinium ester, imidazole, acridiniumsalt and oxalate ester.

Likewise, a bioluminescent compound may be used to label the bindingprotein. Bioluminescence is a type of chemiluminescence found inbiological systems in which a catalytic protein increases the efficiencyof the chemiluminescent reaction. The presence of a bioluminescentprotein is determined by detecting the presence of luminescence.Important bioluminescent compounds for purposes of labeling areluciferin, luciferase and aequorin.

Enzyme labels, such as horseradish peroxidase and alkaline phosphatase,are preferred. When an enzyme label is used, the signal producing systemmust also include a substrate for the enzyme. If the enzymatic reactionproduct is not itself detectable, the SPS will include one or moreadditional reactants so that a detectable product appears.

Assays may be divided into two basic types, heterogeneous andhomogeneous. In heterogeneous assays, the interaction between theaffinity molecule and the analyte does not affect the label, hence, todetermine the amount or presence of analyte, bound label must beseparated from free label. In homogeneous assays, the interaction doesaffect the activity of the label, and therefore analyte levels can bededuced without the need for a separation step.

In general, a kallikrein-binding protein (KBP) may be useddiagnostically in the same way that an antikallikrein antibody is used.Thus, depending on the assay format, it may be used to assay Kallikrein,or by competitive inhibition, other substances which bind Kallikrein.The sample will normally be a biological fluid, such as blood, urine,lymph, semen, milk, or cerebrospinal fluid, or a fraction or derivativethereof, or a biological tissue, in the form of, e.g., a tissue sectionor homogenate. However, the sample conceivably could be (or derivedfrom) a food or beverage, a pharmaceutical or diagnostic composition,soil, or surface or ground water. If a biological fluid or tissue, itmay be taken from a human or other mammal, vertebrate or animal, or froma plant. The preferred sample is blood, or a fraction or derivativethereof.

In one embodiment, the kallikrein-binding protein is insolubilized bycoupling it to a macromolecular support, and kallikrein in the sample isallowed to compete with a known quantity of a labeled or specificallylabelable kallikrein analogue. The “kallikrein analogue” is a moleculecapable of competing with kallikrein for binding to the KBP, and theterm is intended to include kallikrein itself. It may be labeledalready, or it may be labeled subsequently by specifically binding thelabel to a moiety differentiating the kallikrein analogue fromkallikrein. The solid and liquid phases are separated, and the labeledkallikrein analogue in one phase is quantified. The higher the level ofkallikrein analogue in the solid phase, i.e., sticking to the KBP, thelower the level of kallikrein analyte in the sample.

In a “sandwich assay”, both an insolubilized kallikrein-binding protein,and a labeled kallikrein-binding protein are employed. The kallikreinanalyte is captured by the insolubilized kallikrein-binding protein andis tagged by the labeled KBP, forming a tertiary complex. The reagentsmay be added to the sample in either order, or simultaneously. Thekallikrein-binding proteins may be the same or different, and only oneneed be a KBP according to the present invention (the other may be,e.g., an antibody or a specific binding fragment thereof). The amount oflabeled KBP in the tertiary complex is directly proportional to theamount of kallikrein analyte in the sample.

The two embodiments described above are both heterogeneous assays.However, homogeneous assays are conceivable. The key is that the labelbe affected by whether or not the complex is formed.

The kallikrein analyte may act as its own label if a kallikreininhibitor is used as a diagnostic reagent.

A label may be conjugated, directly or indirectly (e.g., through alabeled anti-KBP antibody), covalently (e.g., with SPDP) ornoncovalently, to the kallikrein-binding protein, to produce adiagnostic reagent. Similarly, the kallikrein binding protein may beconjugated to a solid-phase support to form a solid phase (“capture”)diagnostic reagent. Suitable supports include glass, polystyrene,polypropylene, polyethylene, dextran, nylon, amylases, natural andmodified celluloses, polyacrylamides, agaroses, and magnetite. Thenature of the carrier can be either soluble to some extent or insolublefor the purposes of the present invention. The support material may havevirtually any possible structural configuration so long as the coupledmolecule is capable of binding to its target. Thus the supportconfiguration may be spherical, as in a bead, or cylindrical, as in theinside surface of a test tube, or the external surface of a rod.Alternatively, the surface may be flat such as a sheet, test strip, etc.

In Vivo Diagnostic Uses

Kunitz domains that bind very tightly to proteases that are causingpathology can be used for in vivo imaging. Diagnostic imaging of diseasefoci is considered one of the largest commercial opportunities formonoclonal antibodies. This opportunity has not, however, been achieved.Despite considerable effort and resources, to date only one monoclonalantibody-based imaging agent has received regulatory approval. Thedisappointing results obtained with monoclonal antibodies is due inlarge measure to:

-   -   i) Inadequate affinity and/or specificity;    -   ii) Poor penetration to target sites;    -   iii) Slow clearance from nontarget sites;    -   iv) Immunogenicity, most are mouse antibodies; and    -   v) High production cost and poor stability.        These limitations have led most in the diagnostic imaging field        to begin to develop peptide-based imaging agents. While        potentially solving the problems of poor penetration and slow        clearance, peptide-based imaging agents are unlikely to possess        adequate affinity, specificity and in vivo stability to be        useful in most applications.

Engineered proteins are uniquely suited to the requirements for animaging agent. In particular the extraordinary affinity and specificitythat is obtainable by engineering small, stable, human-origin proteindomains having known in vivo clearance rates and mechanisms combine toprovide earlier, more reliable results, less toxicity/side effects,lower production and storage cost, and greater convenience of labelpreparation. Indeed, it should be possible to achieve the goal ofrealtime imaging with engineered protein imaging agents. Thus, aKallikrein-binding protein, e.g., KKII/3#6 (SEQ ID NO:7), may be usedfor localizing sites of excessive pKA activity.

Radio-labelled binding protein may be administered to the human oranimal subject. Administration is typically by injection, e.g.,intravenous or arterial or other means of administration in a quantitysufficient to permit subsequent dynamic and/or static imaging usingsuitable radio-detecting devices. The preferred dosage is the smallestamount capable of providing a diagnostically effective image, and may bedetermined by means conventional in the art, using known radio-imagingagents as a guide.

Typically, the imaging is carried out on the whole body of the subject,or on that portion of the body or organ relevant to the condition ordisease under study. The radio-labelled binding protein has accumulated.The amount of radio-labelled binding protein accumulated at a givenpoint in time in relevant target organs can then be quantified.

A particularly suitable radio-detecting device is a scintillationcamera, such as a gamma camera. A scintillation camera is a stationarydevice that can be used to image distribution of radio-labelled bindingprotein. The detection device in the camera senses the radioactivedecay, the distribution of which can be recorded. Data produced by theimaging system can be digitized. The digitized information can beanalyzed over time discontinuously or continuously. The digitized datacan be processed to produce images, called frames, of the pattern ofuptake of the radio-labelled binding protein in the target organ at adiscrete point in time. In most continuous (dynamic) studies,quantitative data is obtained by observing changes in distributions ofradioactive decay in target organs over time. In other words, atime-activity analysis of the data will illustrate uptake throughclearance of the radio-labelled binding protein by the target organswith time.

Various factors should be taken into consideration in selecting anappropriate radioisotope. The radioisotope must be selected with a viewto obtaining good quality resolution upon imaging, should be safe fordiagnostic use in humans and animals, and should preferably have a shortphysical half-life so as to decrease the amount of radiation received bythe body. The radioisotope used should preferably be pharmacologicallyinert, and, in the quantities administered, should not have anysubstantial physiological effect.

The binding protein may be radio-labelled with different isotopes ofiodine, for example ¹²³I, ¹²⁵I, or ¹³¹I (see for example, U.S. Pat. No.4,609,725). The extent of radio-labeling must, however be monitored,since it will affect the calculations made based on the imaging results(i.e. a diiodinated binding protein will result in twice the radiationcount of a similar monoiodinated binding protein over the same timeframe).

In applications to human subjects, it may be desirable to useradioisotopes other than ¹²⁵I for labelling in order to decrease thetotal dosimetry exposure of the human body and to optimize thedetectability of the labelled molecule (though this radioisotope can beused if circumstances require). Ready availability for clinical-use isalso a factor. Accordingly, for human applications, preferredradio-labels are for example, ^(99m)Tc, ⁶⁷Ga, ⁶⁸Ga, ⁹⁰Y, ¹¹¹In,^(113m)In, ¹²³I, ¹⁸⁶Re, ¹⁸⁸Re or ²¹¹At.

The radio-labelled protein may be prepared by various methods. Theseinclude radio-halogenation by the chloramine-T method or thelactoperoxidase method and subsequent purification by HPLC (highpressure liquid chromatography), for example as described by J.Gutkowska et al in “Endocrinology and Metabolism Clinics of America:(1987) 16 (1):183. Other known method of radio-labelling can be used,such as IODOBEADS™.

There are a number of different methods of delivering the radio-labelledprotein to the end-user. It may be administered by any means thatenables the active agent to reach the agent's site of action in the bodyof a mammal. Because proteins are subject to being digested whenadministered orally, parenteral administration, i.e., intravenoussubcutaneous, intramuscular, would ordinarily be used to optimizeabsorption.

High-affinity, high-specificity inhibitors are also useful for in vitrodiagnostics of excess human pKA activity.

Other Uses

The kallikrein-binding proteins of the present invention may also beused to purify kallikrein from a fluid, e.g., blood. For this purpose,the KBP is preferably immobilized on a solid-phase support. Suchsupports, include those already mentioned as useful in preparing solidphase diagnostic reagents.

Proteins, in general, can be used as molecular weight markers forreference in the separation or purification of proteins byelectrophoresis or chromatography. In many instances, proteins may needto be denatured to serve as molecular weight markers. A second generalutility for proteins is the use of hydrolyzed protein as a nutrientsource. Hydrolyzed protein is commonly used as a growth media componentfor culturing microorganisms, as well as a food ingredient for humanconsumption. Enzymatic or acid hydrolysis is normally carried out eitherto completion, resulting in free amino acids, or partially, to generateboth peptides and amino acids: However, unlike acid hydrolysis,enzymatic hydrolysis (proteolysis) does not remove non-amino acidfunctional groups that may be present: Proteins may also be used toincrease the viscosity of a solution.

The proteins of the present invention may be used for any of theforegoing purposes, as well as for therapeutic and diagnostic purposesas discussed further earlier in this specification.

EXAMPLE 1 Construction of LACI (K1) Library

A synthetic oligonucleotide duplex having NsiI-and MluI-compatible endswas cloned into a parental vector (LACI:III) previously cleaved with theabove two enzymes. The resultant ligated material was transfected byelectroporation into XLIMR (F-) Escherichia coli strain and plated onAmp plates to obtain phage-generating Ap^(R) colonies. The variegationscheme for Phase 1 focuses on the P1 region, and affected residues 13,16, 17, 18 and 19. It allowed for 6.6×10⁵ different DNA sequences(3.1×10⁵ different protein sequences). The library obtained consisted of1.4×10⁶ independent cfu's which is approximately a two foldrepresentation of the whole library. The phage stock generated from thisplating gave a total titer of 1.4×10¹³ pfu's in about 3.9 ml, with eachindependent clone being represented, on average, 1×10⁷ in total and2.6×10⁶ times per ml of phage stock.

To allow for variegation of residues 31, 32, 34 and 39 (phase II),synthetic oligonucleotide duplexes with MluI-and BstEII-compatible endswere cloned into previously cleaved R_(f) DNA derived from one of thefollowing

-   -   i) the parental construction,    -   ii) the phase I library, or    -   iii) display phage selected from the first phase binding to a        given target.        The variegation scheme for phase II allows for 4096 different        DNA sequences (1600 different protein sequences) due to        alterations at residues 31, 32, 34 and 39. The final phase II        variegation is dependent upon the level of variegation remaining        following the three rounds of binding and elution with a given        target in phase I.

The combined possible variegation for both phases equals 2.7×10⁸different DNA sequences or 5.0×10⁷ different protein sequences. Whenpreviously selected display phage are used as the origin of R_(f) DNAfor the phase II variegation, the final level of variegation is probablyin the range of 10⁵ to 10⁶.

EXAMPLE 2 Screening of LACI (K1) Library for Binding to Kallikrein

The overall scheme for selecting a LACI(K1) variant to bind to a givenprotease involves incubation of the phage-display library with thekallikrein-beads of interest in a buffered solution (PBS containing 1mg/ml BSA) followed by washing away the unbound and poorly retaineddisplay-phage variant with PBS containing 0.1% Tween 20. Kallikreinbeads were made by coupling human plasma Kallikrein (Calbiochem, SanDiego, Calif., #420302) to agarose beads using Reactigel (6×) (Pierce,Rockford, Ill., #202606). The more strongly bound display-phage areeluted with a low pH elution buffer, typically citrate buffer (pH 2.0)containing 1 mg/ml BSA, which is immediately neutralized with Trisbuffer to pH 7.5. This process constitutes a single round of selection.

The neutralized eluted display-phage can be either used:

-   -   i) to inoculate an F⁺ strain of E. coli to generate a new        display-phage stock, to be used for subsequent rounds of        selection (so-called conventional screening), or    -   ii) be used directly for another immediate round of selection        with the protease beads (so-called quick screening).        Typically, three rounds of either method, or a combination of        the two, are performed to give rise to the final selected        display-phage from which a representative number are sequenced        and analyzed for binding properties either as pools of        display-phage or as individual clones.

Two phases of selection were performed, each consisting of three roundsof binding and elution. Phase I selection used the phase I library(variegated residues 13, 16, 17, 18, and 19) which went through threerounds of binding and elution against a target protease giving rise to asubpopulation of clones. The R_(f) DNA derived from this selectedsubpopulation was used to generate the Phase II library (addition ofvariegated residues 31, 32, 34 and 39). The 1.8×10⁷ independenttransformants were obtained for each of the phase II libraries. Thephase II libraries underwent three further rounds of binding and elutionwith the same target protease giving rise to the final selectants.

Following two phases of selection against human plasmakallikrein-agarose beads a number (10) of the final selectiondisplay-phage were sequenced. Table 6 shows the amino acids found at thevariegated positions of LACI-K1 in the selected phage. Table 18 showsthe complete sequences of the displayed proteins.

Table 23 shows that KkII/3(D) is a highly specific inhibitor of humanKallikrein. Phage that display the LACI-K1 derivative KkII/3(D) bind toKallikrein beads at least 50-times more than it binds to other proteasetargets.

Preliminary measurements indicate that KKII/3#6 (SEQ ID NO:7) is apotent inhibitor of pKA with K_(i) probably less than 500 pM.

All references, including those to U.S. and foreign patents or patentapplications, and to nonpatent disclosures, are hereby incorporated byreference in their entirety.

TABLE 6 Amino acid sequences of LACI(K1) variants selected for bindingto human plasma kallikrein. 13 16 17 18 19 31 32 34 39(a) KKII/3#1 (SEQID NO: 2) H A S L P E E I E KKII/3#2 (SEQ ID NO: 3) P A N H L E E S GKKII/3#3 (SEQ ID NO: 4) H A N H Q E E T G KKII/3#4 (SEQ ID NO: 5) H A NH Q E Q T A KKII/3#5 (SEQ ID NO: 6) H A S L P E E I G KKII/3#6 (SEQ IDNO: 7) H A N H Q E E S G KKII/3#7 (SEQ ID NO: 8) H A N H Q E E S GKKII/3#8 (SEQ ID NO: 9) H A N H Q E E S G KKII/3#9 (SEQ ID NO: 10) H A NH Q E E S G KKII/3#10 (SEQ ID NO: 11) H G A H L E E I E Consensus H A NH Q E E S/T G (a)Amino acid numbers of variegated residues. LACI(K1)(residues 50-107 of SEQ ID NO: 25) is 58 amino acids long with the P1position being residue number 15 and fixed as lysine in this instance.Whole sequences given in Table 18

TABLE 7 Kallikrein-binding display-phage chosen for further analysis. 1316 17 18 19 31 32 34 39 KKII/3#6 (SEQ ID NO: 7) H A N H Q E E S GKKII/3#5 (SEQ ID NO: 6) H A S L P E E I G KKI/3(b) (SEQ ID NO: 13) P A IH L E E I E KKI/3(a) (SEQ ID NO: 12 R G A H L E E I E LACI(K1) (residues50-107 P A I M K E E I E* of SEQ ID NO: 25) BPTI (SEQ ID NO: 1) P A R II Q T V R** (Note that clones a and b are from the first phase ofscreening and as such have a wild type sequence at residues 31 to 39.*Parental molecule. **Control (bovine pancreatic trypsin inhibitor.)Whole sequences given in Table 18 and Table 17(BPTI)

TABLE 8 Binding Data for Selected Kallikrein-binding Display-Phage.Fraction Relative Display-Phage (a) Bound (b) Binding (c) LACI (residues50-107 4.2 × 10−6 1.0 of SEQ ID NO: 25) BPTI (SEQ ID NO: 1) 2.5 × 10−66.0 KKI/3 (a) (SEQ ID NO: 12) 3.2 × 10−5 761 KKI/3 (b) (SEQ ID NO: 13)2.2 × 10−3 524 KKII/3#5 (SEQ ID NO: 6) 3.9 × 10−3 928 KKII/3#6 (SEQ IDNO: 7) 8.7 × 10−3 2071 (a) Clonal isolates of display-phage. LACI(K1) isthe parental molecule, BPTI (bovine pancreatic trypsin inhibitor) is acontrol and KKII/3(5 and 6) and KKI/3(a and b) were selected by bindingto the target protease, kallikrein. (b) The number of pfu's eluted aftera binding experiment as a fraction of the input number (10¹⁰ pfu's). (c)Fraction bound relative to the parental display-phage, LACI(K1).

TABLE 17 Amino-acid sequence of BPTI         1         2         3         4         51234567890123456789012345678901234567890123456789012345678RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA (SEQ ID NO: 1)

TABLE 18Sequence of LACI-K1 and derivatives that bind human plasma kallikrein         1         2         3         4         51234567890123456789012345678901234567890123456789012345678 LACI-K1 mhsfcafkaddgpckaimkrfffniftrqceefiyggcegnqnrfesleeckkmctrd(residues 50-107 of SEQ ID NO: 25) KKII/3#1mhsfcafkaddgHckASLPrfffniftrqcEEfIyggcEgnqnrfesleeckkmctrd(SEQ ID NO: 2) KKII/3#2mhsfcafkaddgPckANHLrfffniftrqcEEfSyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 3) KKII/3#3mhsfcafkaddgHckANHQrfffniftrqcEEfTyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 4) KKII/3#4mhsfcafkaddgHckANHQrfffniftrqcEQfTyggcAgnqnrfesleeckkmctrd(SEQ ID NO: 5) KKII/3#5mhsfcafkaddgHckASLPrfffniftrqcEEfIyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 6) KKII/3#6mhsfcafkaddgHckANHQrfffniftrqcEEfSyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 7) KKII/3#7mhsfcafkaddgHckANHQrfffniftrqcEEfSyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 8) KKII/3#8mhsfcafkaddgHckANHQrfffniftrqcEEfSyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 9) KKII/3#9mhsfcafkaddgHckANHQrfffniftrqcEEfSyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 10) KKII/3#10mhsfcafkaddgHckGAHLrfffniftrqcEEfIyggcEgnqnrfesleeckkmctrd(SEQ ID NO: 11) KKII/3 (a)mhsfcafkaddgRckGAHLrfffniftrqceefiyggcegnqnrfesleeckkmctrd(SEQ ID NO: 12) KKII/3 (b)mhsfcafkaddgPckAIHLrfffniftrqceefiyggcegnqnrfesleeckkmctrd(SEQ ID NO: 13) KKII/3#CmhsfcafkaddgHckANHQrfffniftrqcEEfSyggcGgnqnrfesleeckkmctrd(SEQ ID NO: 14)

TABLE 21 Variegation of LACI-K1

The segment from NsiI to MluI gives 65,536 DNA sequences and 31,200protein sequences. Second group of variegation gives 21,840 and 32,768variants. This variegation can go in on a fragment having MluI and oneof AgeI, BstBI, or XbaI ends. Because of the closeness between codon 42and the 3′ restriction site, one will make a self-primingoligonucleotide, fill in, and cut with MluI and, for example, BstBI.Total variants are 2.716 × 10⁹ and 8.59 × 10⁹.

TABLE 23 Specificity Results Trypsin, Target two Display PlasminThrombin Kallikrein Trypsin washes LACI-K¹ 1.0 1.0 1.0 1.0 1.0KkII/3(D)² 3.4 1.5 196. 2.0 1.4 BPTI::III³ (88)⁴ (1.1) (1.7) (0.3) (0.8)numbers refer to relative binding of phage display clo4nes compared tothe parental phage display. The KkII/3(D)(Kallikrein) clone retains theparental molecule's affinity for trypsin. ¹Displayed on M13 III.²Selected for plasma kallikrein binding. ³Control. ⁴BPTI relative toLACI.

TABLE 40 Coordinates of BPTI (1TPA) N ARG 1 11.797 100.411 6.463 CA ARG1 12.697 101.495 6.888 C ARG 1 13.529 101.329 8.169 O ARG 1 14.755101.605 8.115 CB ARG 1 12.037 102.886 6.801 CG ARG 1 13.107 103.9696.578 CD ARG 1 12.560 105.405 6.648 NE ARG 1 13.682 106.329 6.443 CZ ARG1 13.570 107.597 6.106 NH1 ARG 1 12.380 108.144 5.959 NH2 ARG 1 14.657108.320 5.922 N PRO 2 12.931 101.060 9.332 CA PRO 2 13.662 101.10110.617 C PRO 2 14.678 99.990 10.886 O PRO 2 14.239 98.887 11.277 CB PRO2 12.604 100.958 11.726 CG PRO 2 11.250 100.694 11.051 CD PRO 2 11.489100.823 9.539 N ASP 3 15.885 100.463 11.149 CA ASP 3 17.078 99.90911.973 C ASP 3 17.125 98.489 12.483 O ASP 3 18.085 97.801 12.106 CB ASP3 17.819 100.822 12.981 CG ASP 3 18.284 100.049 14.210 OD1 ASP 3 17.667100.236 15.287 OD2 ASP 3 19.492 99.710 14.278 N PHE 4 16.069 97.94913.050 CA PHE 4 15.939 96.466 13.148 C PHE 4 15.865 95.753 11.765 O PHE4 16.126 94.534 11.580 CB PHE 4 14.817 96.062 14.145 CG PHE 4 13.38696.292 13.636 CD1 PHE 4 12.801 95.382 12.783 CD2 PHE 4 12.735 97.44713.940 CE1 PHE 4 11.539 95.602 12.260 CE2 PHE 4 11.482 97.684 13.408 CZPHE 4 10.879 96.748 12.582 N CYS 5 15.456 96.498 10.755 CA CYS 5 15.35895.949 9.416 C CYS 5 16.745 95.732 8.840 O CYS 5 16.856 95.011 7.838 CBCYS 5 14.653 96.970 8.534 SG CYS 5 12.907 97.271 8.905 N LEU 6 17.76596.247 9.497 CA LEU 6 19.110 96.026 9.002 C LEU 6 19.777 94.885 9.731 OLEU 6 20.896 94.493 9.322 CB LEU 6 19.986 97.263 9.235 CG LEU 6 19.43898.493 8.493 CD1 LEU 6 20.291 99.703 8.860 CD2 LEU 6 19.261 98.356 6.971N GLU 7 19.122 94.342 10.725 CA GLU 7 19.755 93.241 11.464 C GLU 719.711 91.890 10.740 O GLU 7 18.873 91.648 9.852 CB GLU 7 19.232 93.16312.914 CG GLU 7 19.336 94.483 13.695 CD GLU 7 18.778 94.225 15.092 OE1GLU 7 18.815 93.054 15.548 OE2 GLU 7 17.924 95.019 15.561 N PRO 8 20.76591.108 10.862 CA PRO 8 20.839 89.797 10.262 C PRO 8 19.790 88.842 10.860O PRO 8 19.233 89.114 11.944 CB PRO 8 22.244 89.267 10.608 CG PRO 822.754 90.131 11.757 CD PRO 8 21.882 91.377 11.769 N PRO 9 19.319 87.91110.080 CA PRO 9 18.232 87.056 10.487 C PRO 9 18.694 86.135 11.628 O PRO9 19.855 85.673 11.592 CB PRO 9 17.905 86.208 9.266 CG PRO 9 19.17186.263 8.426 CD PRO 9 19.774 87.618 8.743 N TYR 10 17.829 85.920 12.619CA TYR 10 18.072 85.128 13.831 C TYR 10 17.277 83.837 13.923 O TYR 1016.039 83.903 14.101 CB TYR 10 17.700 86.057 15.008 CG TYR 10 18.10585.479 16.355 CD1 TYR 10 17.163 85.154 17.302 CD2 TYR 10 19.449 85.29116.610 CE1 TYR 10 17.586 84.599 18.519 CE2 TYR 10 19.872 84.762 17.821CZ TYR 10 18.945 84.405 18.771 OH TYR 10 19.413 83.745 19.968 N THR 1117.930 82.728 13.743 CA THR 11 17.250 81.464 13.910 C THR 11 16.90581.173 15.365 O THR 11 15.806 80.629 15.663 CB THR 11 18.157 80.34213.426 OG1 THR 11 18.374 80.467 12.011 CG2 THR 11 17.587 78.955 13.770 NGLY 12 17.800 81.499 16.276 CA GLY 12 17.530 81.172 17.717 C GLY 1217.795 79.707 18.130 O GLY 12 18.093 78.812 17.294 N PRO 13 17.59479.422 19.438 CA PRO 13 18.020 78.175 20.067 C PRO 13 17.028 77.02419.943 O PRO 13 17.521 75.872 19.887 CB PRO 13 18.118 78.476 21.544 CGPRO 13 17.139 79.617 21.758 CD PRO 13 17.023 80.360 20.414 N CYS 1415.735 77.328 19.666 CA CYS 14 14.732 76.275 19.385 C CYS 14 14.88075.629 18.020 O CYS 14 15.608 76.158 17.146 CB CYS 14 13.299 76.71719.613 SG CYS 14 12.983 77.300 21.278 N LYS 15 14.500 74.402 17.967 CALYS 15 14.776 73.485 16.889 C LYS 15 13.544 73.079 16.047 O LYS 1513.540 71.988 15.436 CB LYS 15 15.423 72.254 17.559 CG LYS 15 16.81672.596 18.149 CD LYS 15 17.559 71.326 18.616 CE LYS 15 18.900 71.63619.321 NZ LYS 15 19.518 70.412 19.904 N ALA 16 12.618 73.966 15.829 CAALA 16 11.683 73.785 14.691 C ALA 16 12.409 74.246 13.418 O ALA 1613.458 74.945 13.471 CB ALA 16 10.368 74.627 14.903 N ARG 17 11.87273.853 12.310 CA ARG 17 12.256 74.420 11.018 C ARG 17 11.079 75.21510.439 O ARG 17 10.278 74.719 9.613 CB ARG 17 12.733 73.245 10.174 CGARG 17 13.392 73.661 8.858 CD ARG 17 12.294 74.044 7.852 NE ARG 1712.786 73.577 6.649 CZ ARG 17 12.596 72.435 6.095 NH1 ARG 17 11.63771.610 6.379 NH2 ARG 17 13.299 72.211 5.023 N ILE 18 10.949 76.45710.831 CA ILE 18 9.848 77.334 10.377 C ILE 18 10.312 78.435 9.443 O ILE18 11.321 79.098 9.777 CB ILE 18 9.158 77.976 11.596 CG1 ILE 18 8.47976.864 12.430 CG2 ILE 18 8.132 79.053 11.235 CD1 ILE 18 8.302 77.40913.857 N ILE 19 9.724 78.469 8.238 CA ILE 19 10.176 79.438 7.218 C ILE19 9.523 80.797 7.401 O ILE 19 8.274 80.911 7.406 CB ILE 19 10.07478.910 5.754 CG1 ILE 19 10.860 77.594 5.658 CG2 ILE 19 10.525 79.9814.702 CD1 ILE 19 10.362 76.681 4.550 N ARG 20 10.369 81.764 7.648 CA ARG20 9.967 83.160 7.870 C ARG 20 10.707 84.063 6.893 O ARG 20 11.53783.519 6.130 CB ARG 20 10.349 83.584 9.300 CG ARG 20 9.573 82.818 10.384CD ARG 20 8.086 83.272 10.386 NE ARG 20 7.308 82.535 11.412 CZ ARG 207.174 83.017 12.653 NH1 ARG 20 7.772 84.156 13.006 NH2 ARG 20 6.60682.289 13.595 N TYR 21 10.399 85.366 6.904 CA TYR 21 10.990 86.415 6.062C TYR 21 11.783 87.398 6.869 O TYR 21 11.415 87.709 8.041 CB TYR 219.927 87.254 5.321 CG TYR 21 9.227 86.344 4.286 CD1 TYR 21 8.248 85.4454.687 CD2 TYR 21 9.646 86.387 2.959 CE1 TYR 21 7.676 84.603 3.763 CE2TYR 21 9.069 85.549 2.012 CZ TYR 21 8.078 84.673 2.405 OH TYR 21 7.55783.773 1.412 N PHE 22 12.796 87.894 6.215 CA PHE 22 13.615 88.967 6.804C PHE 22 13.987 89.932 5.698 O PHE 22 14.116 89.477 4.531 CB PHE 2214.907 88.520 7.581 CG PHE 22 16.075 88.032 6.669 CD1 PHE 22 17.13488.870 6.407 CD2 PHE 22 15.985 86.820 6.026 CE1 PHE 22 18.117 88.5105.493 CE2 PHE 22 16.971 86.465 5.087 CZ PHE 22 18.026 87.309 4.827 N TYR23 14.114 91.168 6.073 CA TYR 23 14.585 92.201 5.205 C TYR 23 16.09092.078 4.923 O TYR 23 16.917 92.192 5.837 CB TYR 23 14.153 93.589 5.740CG TYR 23 14.412 94.670 4.674 CD1 TYR 23 15.332 95.661 4.931 CD2 TYR 2313.831 94.573 3.433 CE1 TYR 23 15.673 96.561 3.951 CE2 TYR 23 14.12695.511 2.461 CZ TYR 23 15.051 96.500 2.711 OH TYR 23 15.328 97.524 1.731N ASN 24 16.465 91.884 3.687 CA ASN 24 17.855 91.855 3.252 C ASN 2418.214 93.189 2.601 O ASN 24 17.796 93.529 1.451 CB ASN 24 18.069 90.7292.240 CG ASN 24 19.546 90.661 1.887 OD1 ASN 24 20.363 91.402 2.468 ND2ASN 24 19.880 89.455 1.644 N ALA 25 18.758 94.021 3.466 CA ALA 25 19.11595.402 3.073 C ALA 25 20.153 95.346 1.943 O ALA 25 20.214 96.277 1.110CB ALA 25 19.718 96.214 4.248 N LYS 26 20.926 94.294 1.871 CA LYS 2621.927 94.209 .795 C LYS 26 21.316 93.971 −.576 O LYS 26 21.631 94.746−1.505 CB LYS 26 23.192 93.345 1.081 CG LYS 26 24.224 94.036 1.988 CDLYS 26 25.450 93.125 2.200 CE LYS 26 26.558 93.805 3.024 NZ LYS 2627.649 92.853 3.266 N ALA 27 20.301 93.136 −.638 CA ALA 27 19.535 92.893−1.842 C ALA 27 18.417 93.896 −2.055 O ALA 27 17.769 94.008 −3.140 CBALA 27 18.965 91.498 −1.663 N GLY 28 18.108 94.574 −1.014 CA GLY 2816.876 95.398 −1.159 C GLY 28 15.598 94.564 −1.366 O GLY 28 14.60595.041 −1.966 N LEU 29 15.540 93.437 −.697 CA LEU 29 14.302 92.689 −.621C LEU 29 14.113 91.764 .573 O LEU 29 15.091 91.447 1.290 CB LEU 2913.946 92.088 −1.983 CG LEU 29 14.560 90.736 −2.317 CD1 LEU 29 14.42890.452 −3.825 CD2 LEU 29 15.947 90.475 −1.753 N CYS 30 12.929 91.251.701 CA CYS 30 12.631 90.232 1.679 C CYS 30 12.973 88.827 1.225 O CYS 3012.555 88.398 .118 CB CYS 30 11.200 90.387 2.252 SG CYS 30 10.933 92.0092.993 N GLN 31 13.803 88.164 2.043 CA GLN 31 14.137 86.787 1.847 C GLN31 13.585 85.869 2.933 O GLN 31 13.386 86.287 4.096 CB GLN 31 15.66886.613 1.685 CG GLN 31 16.217 87.696 .795 CD GLN 31 17.411 87.066 .084OE1 GLN 31 18.580 87.572 .152 NE2 GLN 31 16.976 86.163 −.802 N THR 3213.640 84.623 2.640 CA THR 32 13.288 83.547 3.599 C THR 32 14.502 83.0084.376 O THR 32 15.653 83.038 3.878 CB THR 32 12.607 82.379 2.857 OG1 THR32 13.481 81.840 1.887 CG2 THR 32 11.287 82.754 2.182 N PHE 33 14.27782.464 5.547 CA PHE 33 15.348 81.924 6.396 C PHE 33 14.664 80.984 7.337O PHE 33 13.406 81.039 7.354 CB PHE 33 16.052 83.054 7.174 CG PHE 3315.292 83.602 8.392 CD1 PHE 33 15.668 83.194 9.661 CD2 PHE 33 14.29984.545 8.255 CE1 PHE 33 15.040 83.692 10.779 CE2 PHE 33 13.664 85.0649.397 CZ PHE 33 14.036 84.631 10.661 N VAL 34 15.421 80.121 8.005 CA VAL34 14.817 79.158 8.946 C VAL 34 14.792 79.652 10.385 O VAL 34 15.82480.145 10.871 CB VAL 34 15.603 77.860 8.945 CG1 VAL 34 15.195 76.93710.125 CG2 VAL 34 15.430 77.129 7.611 N TYR 35 13.618 79.811 10.941 CATYR 35 13.427 80.274 12.288 C TYR 35 13.079 79.099 13.188 O TYR 3512.406 78.147 12.731 CB TYR 35 12.330 81.337 12.313 CG TYR 35 11.87081.698 13.742 CD1 TYR 35 12.758 82.213 14.672 CD2 TYR 35 10.537 81.52914.090 CE1 TYR 35 12.316 82.567 15.958 CE2 TYR 35 10.082 81.920 15.351CZ TYR 35 10.986 82.455 16.276 OH TYR 35 10.533 82.900 17.569 N GLY 3613.843 78.988 14.257 CA GLY 36 13.813 77.777 15.086 C GLY 36 12.60877.757 16.045 O GLY 36 12.258 76.684 16.583 N GLY 37 11.827 78.80916.058 CA GLY 37 10.533 78.722 16.717 C GLY 37 10.571 79.339 18.109 OGLY 37 9.500 79.680 18.662 N CYS 38 11.653 79.933 18.487 CA CYS 3811.521 80.813 19.692 C CYS 38 12.516 81.957 19.703 O CYS 38 13.60981.759 19.130 CB CYS 38 11.705 80.016 21.020 SG CYS 38 13.319 79.23021.236 N ARG 39 12.201 82.955 20.477 CA ARG 39 13.042 84.091 20.782 CARG 39 13.345 84.908 19.525 O ARG 39 14.479 85.415 19.364 CB ARG 3914.338 83.591 21.467 CG ARG 39 14.123 83.002 22.885 CD ARG 39 15.50982.671 23.502 NE ARG 39 15.363 82.331 24.931 CZ ARG 39 16.144 81.40325.524 NH1 ARG 39 17.181 80.838 24.899 NH2 ARG 39 15.926 81.022 26.767 NALA 40 12.336 85.093 18.668 CA ALA 40 12.469 85.896 17.438 C ALA 4013.003 87.295 17.694 O ALA 40 12.459 87.974 18.591 CB ALA 40 11.08286.134 16.840 N LYS 41 13.780 87.825 16.770 CA LYS 41 14.069 89.24616.766 C LYS 41 13.050 89.929 15.884 O LYS 41 12.110 89.279 15.385 CBLYS 41 15.514 89.487 16.297 CG LYS 41 16.414 88.775 17.308 CD LYS 4117.893 89.161 17.266 CE LYS 41 18.524 88.784 18.640 NZ LYS 41 19.97788.978 18.595 N ARG 42 13.185 91.205 15.759 CA ARG 42 12.207 91.98614.989 C ARG 42 12.282 91.935 13.459 O ARG 42 11.214 91.904 12.783 CBARG 42 12.066 93.440 15.465 CG ARG 42 11.365 93.469 16.839 CD ARG 4211.248 94.923 17.264 NE ARG 42 12.630 95.393 17.419 CZ ARG 42 13.03496.670 17.567 NH1 ARG 42 12.191 97.681 17.582 NH2 ARG 42 14.344 96.96417.686 N ASN 43 13.432 91.638 12.944 CA ASN 43 13.534 91.297 11.513 CASN 43 13.074 89.873 11.164 O ASN 43 13.896 88.965 10.939 CB ASN 4314.973 91.612 11.028 CG ASN 43 14.962 91.773 9.511 OD1 ASN 43 13.86791.977 8.926 ND2 ASN 43 16.144 91.851 8.961 N ASN 44 11.803 89.57811.367 CA ASN 44 11.254 88.237 11.328 C ASN 44 9.754 88.326 11.025 O ASN44 8.985 88.836 11.875 CB ASN 44 11.592 87.487 12.662 CG ASN 44 10.99586.079 12.769 OD1 ASN 44 9.967 85.727 12.165 ND2 ASN 44 11.677 85.16513.350 N PHE 45 9.338 88.074 9.788 CA PHE 45 7.939 88.332 9.277 C PHE 457.255 87.073 8.777 O PHE 45 7.934 86.052 8.515 CB PHE 45 7.943 89.3818.158 CG PHE 45 8.609 90.681 8.657 CD1 PHE 45 9.962 90.922 8.445 CD2 PHE45 7.851 91.618 9.326 CE1 PHE 45 10.538 92.109 8.899 CE2 PHE 45 8.43392.808 9.759 CZ PHE 45 9.773 93.056 9.544 N LYS 46 5.953 87.013 8.850 CALYS 46 5.307 85.750 8.528 C LYS 46 4.957 85.669 7.063 O LYS 46 4.81684.538 6.573 CB LYS 46 4.008 85.607 9.317 CG LYS 46 4.338 84.938 10.654CD LYS 46 3.144 85.117 11.573 CE LYS 46 3.348 84.392 12.912 NZ LYS 462.160 84.624 13.772 N SER 47 5.091 86.774 6.384 CA SER 47 4.904 86.7764.924 C SER 47 5.754 87.843 4.273 O SER 47 6.210 88.797 4.983 CB SER 473.418 87.035 4.542 OG SER 47 3.126 80.431 4.812 N ALA 48 6.000 87.6522.979 CA ALA 48 6.785 88.690 2.344 C ALA 48 6.089 90.062 2.370 O ALA 486.728 91.153 2.416 CB ALA 48 7.020 88.246 .910 N GLU 49 4.760 90.0492.411 CA GLU 49 4.004 91.319 2.332 C GLU 49 4.141 92.115 3.621 O GLU 494.288 93.368 3.569 CB GLU 49 2.477 91.014 2.129 CG GLU 49 2.093 90.462.742 CD GLU 49 2.593 89.033 .538 OE1 GLU 49 2.701 88.254 1.524 OE2 GLU49 2.618 88.541 −.630 N ASP 50 4.098 91.367 4.747 CA ASP 50 4.316 92.0366.061 C ASP 50 5.694 92.642 6.098 O ASP 50 5.807 93.832 6.441 CB ASP 504.244 91.148 7.311 CG ASP 50 2.836 90.713 7.693 OD1 ASP 50 1.831 91.1837.108 OD2 ASP 50 2.725 89.630 8.316 N CYS 51 6.660 91.834 5.675 CA CYS51 8.069 92.253 5.611 C CYS 51 8.278 93.500 4.739 O CYS 51 8.797 94.5415.243 CB CYS 51 8.955 91.080 5.141 SG CYS 51 10.694 91.506 4.989 N MET52 7.678 93.467 3.554 CA MET 52 7.777 94.629 2.704 C MET 52 7.113 95.8613.268 O MET 52 7.730 96.945 3.202 CB MET 52 7.489 94.389 1.189 CG MET 528.547 95.004 .261 SD MET 52 9.677 93.778 −.404 CE MET 52 8.424 92.566−.868 N ARG 53 5.939 95.729 3.847 CA ARG 53 5.276 96.896 4.444 C ARG 536.066 97.454 5.604 O ARG 53 6.260 98.691 5.654 CB ARG 53 3.886 96.4624.982 CG ARG 53 2.861 97.572 5.264 CD ARG 53 1.424 97.032 5.029 NE ARG53 1.279 95.906 5.894 CZ ARG 53 1.027 94.612 5.694 NH1 ARG 53 .68694.084 4.520 NH2 ARG 53 1.167 93.823 6.747 N THR 54 6.627 96.618 6.444CA THR 54 7.462 97.165 7.516 C THR 54 8.830 97.720 7.119 O THR 54 9.26698.747 7.690 CB THR 54 7.674 96.154 8.624 OG1 THR 54 6.377 95.698 8.972CG2 THR 54 8.395 96.794 9.843 N CYS 55 9.580 96.927 6.394 CA CYS 5510.971 97.234 6.147 C CYS 55 11.291 97.818 4.797 O CYS 55 12.436 98.3204.690 CB CYS 55 11.850 96.040 6.455 SG CYS 55 11.943 95.674 8.255 N GLY56 10.514 97.479 3.790 CA GLY 56 10.957 97.710 2.392 C GLY 56 11.22899.190 2.152 O GLY 56 10.367 100.002 2.539 N GLY 57 12.461 99.566 1.946CA GLY 57 12.800 100.986 2.017 C GLY 57 13.886 101.219 3.058 O GLY 5714.039 102.363 3.552 N ALA 58 14.615 100.141 3.414 CA ALA 58 15.722100.266 4.422 C ALA 58 17.104 99.977 3.828 O ALA 58 18.036 100.786 4.093CB ALA 58 15.483 99.453 5.728 OXT ALA 58 17.207 99.280 2.788

TABLE 50 Places in BPTI where disulfides are plausible Limit on Ca-Ca is9.0, on Cb-Cb is 6.5 Limit on Ca-Cb is 7.5 Res#1 Res#2 A-A A1-B2 A2-B1B-B ARG 1 GLY 57 4.90 4.71 5.20 4.62 PRO 2 CYS 5 5.56 4.73 6.17 5.50 PHE4 ARG 42 6.11 5.43 4.91 4.02 PHE 4 ASN 43 5.93 5.38 5.59 5.44 CYS 5 TYR23 5.69 4.53 5.82 4.41 CYS 5 CYS 55 5.62 4.59 4.40 3.61 CYS 5 ALA 586.61 5.09 5.38 3.84 LEU 6 ALA 25 5.96 4.80 6.50 5.10 LEU 6 ALA 58 7.105.97 7.10 6.11 GLU 7 ASN 43 6.52 5.07 6.16 4.91 PRO 9 PHE 22 6.21 4.655.66 4.14 PRO 9 PHE 33 7.17 5.63 5.76 4.21 PRO 9 ASN 43 6.41 5.63 7.076.40 TYR 10 LYS 41 6.45 5.62 5.14 4.27 THR 11 VAL 34 5.99 6.35 5.71 5.72THR 11 GLY 36 5.18 4.80 5.31 4.75 GLY 12 CYS 14 5.88 6.43 5.56 5.75 GLY12 GLY 36 5.68 4.66 5.29 4.55 GLY 12 CYS 38 6.34 6.80 4.90 5.49 GLY 12ARG 39 6.17 5.49 4.83 4.35 CYS 14 ALA 16 6.13 6.47 5.95 5.93 CYS 14 GLY36 4.65 3.79 4.68 4.25 CYS 14 GLY 37 5.54 5.42 4.48 4.32 CYS 14 CYS 385.57 5.08 4.47 3.92 ALA 16 ILE 18 5.88 5.79 5.30 4.86 ALA 16 GLY 37 5.464.38 4.48 3.27 ARG 17 VAL 34 5.77 5.23 6.39 5.57 ILE 18 ARG 20 6.34 6.366.44 6.18 ILE 18 TYR 35 5.01 5.09 4.90 4.68 ILE 18 GLY 37 6.53 6.42 5.355.33 ILE 19 THR 32 6.30 5.79 6.04 5.18 ARG 20 TYR 35 6.31 5.35 5.42 4.25ARG 20 ASN 44 6.28 6.66 5.16 5.30 TYR 21 CYS 30 6.04 5.51 5.43 4.57 TYR21 PHE 45 4.83 4.74 4.56 4.06 TYR 21 ALA 48 6.06 6.76 4.56 5.38 TYR 21CYS 51 6.54 5.17 5.34 3.95 PHE 22 PHE 33 7.26 6.41 6.72 5.60 PHE 22 ASN43 5.25 5.17 5.01 4.63 TYR 23 ASN 43 6.46 5.87 6.24 5.70 TYR 23 CYS 516.53 5.74 6.23 5.80 TYR 23 CYS 55 6.27 4.88 4.86 3.44 TYR 23 ALA 58 8.187.33 6.98 6.01 ASN 24 ALA 27 5.46 5.05 4.85 4.08 ASN 24 GLN 31 6.44 5.895.58 4.80 ALA 25 ALA 58 6.08 6.05 5.69 5.53 ALA 27 LEU 29 5.38 5.65 4.925.06 CYS 30 ALA 48 6.08 6.00 4.73 4.88 CYS 30 CYS 51 6.35 5.12 4.96 3.72CYS 30 MET 52 6.63 6.63 5.47 5.56 TYR 35 ASN 44 8.31 7.45 7.05 6.20 ALA40 ASN 44 6.65 5.11 5.90 4.42 LYS 41 ASN 44 6.21 5.11 6.66 5.71 PHE 45ASP 50 6.10 5.04 4.96 4.19 PHE 45 CYS 51 5.37 5.07 3.84 3.61 LYS 46 ASP50 6.83 5.63 7.21 5.90 SER 47 GLU 49 5.31 5.63 4.86 4.75 SER 47 ASP 505.41 5.02 5.30 5.03 MET 52 GLY 56 4.44 3.58 4.95 3.71 CYS 55 ALA 58 5.895.05 6.08 5.04

TABLE 55 Shortened Kunitz domains to bind plasma kallikrein          11111111122222222223333333333444444444455555555 (SEQ ID NO: 1)123456789012345678901234567890123456789012345678912345678RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA BPTIMHSFCAFKADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEECKKMCTRD LACI-K1(residues 50-107 of SEQ ID NO: 25) ShpKa#1:Plasma Kallikrein binder from shortened BPTI

(SEQ ID NO: 17) ShpKa#2: Plasma Kallikrein binder from shortened BPTI

(SEQ ID NO: 18) ShpKa#3: Plasma Kallikrein binder from shortened BPTI

(SEQ ID NO: 19) ShpKa#4: Plasma Kallikrein binder from shortened LACI-K1

(SEQ ID NO: 20) Convert F₂₁ to CYS to allow disulfide to C₃₀. ShpKa#5:Plasma Kallikrein binder from shortened LACI-K1 #2

(SEQ ID NO: 21) Shorten the loop between 21 and 30. ShpKa#6:Plasma Kallikrein binder from shortened LACI-K1 #3

(SEQ ID NO: 22) R20C and Y35C to allow third disulfide. ShpKa#7:Plasma Kallikrein binder from shortened LACI0K1 #4

(SEQ ID NO: 23)Change 24-27 to DVTE (subseq. found in several KuDoms) toreduce positive charge. ShpKa#8:Plasma Kallikrein binder from shortened LACI-K1 #5

(SEQ ID NO: 24)Change 24-27 to NPDA (found in Drosophila funebris KuDom)to get a proline into loop.

TABLE 100 Sequence of whole LACI:  1 MIYTMKKVHA LWASVCLLLN LAPAPLNAds eedeehtiit dtelpplklM(SEQ ID NO: 25) 51 HSFCAFKADD GPCKAIMKRF FFNIFTRQCE EFIYGGCEGN QNRFESLEEC101 KKMCTRDnan riikttlqqe kpdfcfleed pgicrgyitr yfynngtkqc151 erfkyggclg nmnnfetlee cknicedqpn gfqvdnygtq lnavnnsltp201 qstkvpslfe fhgpswcltp adrglcrane nrfyynsvig kcrpfkysgc251 ggnennftsk qeclrackkg fiqriskggl iktkrkrkkq rvkiayeeif 301 vknm  Thesignal sequence (1-28) is uppercase and underscored LACI-K1 is uppercaseLACI-K2 is underscored LACI-K3 is bold

TABLE 103 LACI-K1 derivatives that bind and inhibit human plasmaKallikrein 13 14 15 16 17 18 19 31 32 34 39(a) KKII/3#1 (SEQ ID NO: 2) HC K A S L P E E I E KKII/3#2 (SEQ ID NO: 3) P C K A N H L E E S GKKII/3#3 (SEQ ID NO: 4) H C K A N H Q E E T G KKII/3#4 (SEQ ID NO: 5) HC K A N H Q E Q T A KKII/3#5 (SEQ ID NO: 6) H C K A S L P E E I GKKII/3#6 (SEQ ID NO: 7) H C K A N H Q E E S G KKII/3#7 (SEQ ID NO: 8) HC K A N H Q E E S G KKII/3#8 (SEQ ID NO: 9) H C K A N H Q E E S GKKII/3#9 (SEQ ID NO: 10) H C K A N H Q E E S G KKII/3#10 (SEQ ID NO: 11)H C K G A H L E E I E Consensus H C K A N H Q E E S/T G Fixed C KAbsolute E Strong preference H A H E Good selection N Q G Some selectionS/T

TABLE 202 vgDNA for LACI-D1 tovary residues 10, 11, 13, 15, 16, 17, & 19for pKA in view of previous selections.

DNA: 131,072 protein: 78.848

TABLE 204 Variation of Residues 31, 32, 34, 39, 40, 41, and42 for pKA in view of previous selections.

There are 131,072 DNA sequences and 70,304 protein sequences.

TABLE 220 Cα-Cα distances in P1 region of BPTI T11 G12 P13 C14 K15 A16R17 I18 I19 R20 Q31 T32 V34 G12 3.8 P13 7.0 3.8 C14 8.0 5.9 3.9 K15 8.98.2 6.5 3.7 A16 9.5 9.9 9.4 6.1 3.8 R17 9.1 10.9 11.4 8.9 6.5 3.8 I189.2 11.3 12.7 10.3 9.0 5.9 3.8 I19 10.0 12.9 15.1 13.4 12.2 9.5 6.6 3.8R20 9.6 12.6 15.4 14.2 14.1 11.7 9.6 6.3 3.8 Y21 11.2 14.4 17.7 17.117.3 15.3 13.0 10.1 7.1 3.9 Q31 13.6 17.2 20.5 20.5 20.1 18.4 15.5 13.49.9 8.2 T32 11.2 14.9 18.0 17.4 16.7 14.9 11.8 9.8 6.3 5.4 3.8 V34 6.09.4 11.6 10.8 9.8 8.5 5.8 5.5 5.0 6.4 10.4 7.1

TABLE 1017 High specificity plasma Kallikrein inhibitors LACI-K1MHSFCAFKADDGPCKAIMKRFFFNIFTRQCEEFTYGGCEGNQNRFESL EECKKMCTRD(residues 50-107 of SEQ ID NO: 25) KKII/3#7mhsfcafkaddgHckANHQrfffniftrqcEEfSyggcGgnqnrfesl eeckkmctrd(SEQ ID NO: 8) KKII/3#7-K15AmhsfcafkaddgHcaANHQrfffniftrqcEEfSyggcGgnqnrfesl eeckkmctrd(SEQ ID NO: 31)References Cited

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1. A pharmaceutical composition comprising a kallikrein inhibitingprotein and a pharmaceutically acceptable carrier, wherein thekallikrein inhibiting protein comprises a non-naturally occurring Kunitzdomain, said Kunitz domain having disulfide bonds at Cys5-Cys55,Cys14-Cys38, and Cys30-Cys51 and further having: amino acid number 13selected from the group consisting of His and Pro; amino acid number 14as Cys; amino acid number 16 selected from the group consisting of Alaand Gly; amino acid number 17 selected from the group consisting of Ala,Asn, and Ser; amino acid number 18 selected from the group consisting ofHis and Leu; amino acid number 19 selected from the group consisting ofGln, Leu, and Pro; amino acid number 31 as Glu; amino acid number 32selected from the group consisting of Glu and Gln; amino acid number 34selected from the group consisting of Ser, Thr, and Ile; and amino acidnumber 39 selected from the group consisting of Gly, Glu, and Ala,wherein the above amino acids are numbered to correspond to thenumbering of amino acid residues of bovine pancreatic trypsin inhibitor(BPTI) (SEQ ID NO:1), and wherein the kallikrein inhibiting proteinbinds plasma kallikrein with a Ki less than 500 pM.
 2. Thepharmaceutical composition of claim 1, wherein the Kunitz domain furtherhas: amino acid number 15 selected from the group consisting of Lys andArg, wherein amino acids are numbered to correspond to the numbering ofamino acid residues of bovine pancreatic trypsin inhibitor (BPTI) (SEQID NO: 1).
 3. The pharmaceutical composition of claim 1, wherein theKunitz domain is selected from the group consisting of SEQ ID NO:2, SEQID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ IDNO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:13, SEQ IDNO:14, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:27, SEQ ID NO:28, SEQ IDNO:64, and SEQ ID NO:66.
 4. The pharmaceutical composition of claim 1,wherein the kallikrein inhibiting protein binds plasma kallikrein with aKi less than 50 pM.
 5. The pharmaceutical composition of claim 1,wherein the kallikrein inhibiting protein inhibits plasma kallikreinactivity.
 6. The pharmaceutical composition of claim 1, wherein thecomposition is for systemic or topical administration.
 7. Thepharmaceutical composition of claim 1, wherein the composition is foradministration parenterally.
 8. The pharmaceutical composition of claim1, wherein the composition is for administration intravenously,intradermally, intramuscularly, intraperitoneally, intranasally,transdermally, orally or buccally.
 9. The pharmaceutical composition ofclaim 1, wherein the composition is for administration by bolusinjection or by gradual perfusion over time.
 10. The pharmaceuticalcomposition of claim 1, wherein the composition is for administrationsubcutaneously.
 11. The pharmaceutical composition of claim 1, whereinthe composition is for administration to a human.
 12. The pharmaceuticalcomposition of claim 1, wherein the composition is for administration ina single dose or in multiple doses.